Payroll overview

Payroll is where you pay the people who work for you in the United States. You keep a record of each employee, tell Bokapsys how and how often you pay them, and run payroll each pay period. For every pay run Bokapsys works out each person’s gross pay, the taxes to take off their pay, the taxes you owe as the employer, and their take-home pay. It then records the whole run in your books, produces a payslip for each person and builds the bank file you upload to pay them.

This page explains what Payroll covers, who can use it, what the setup checklist on the Payroll Dashboard is telling you, and the order to do things in for your first payroll.

A few words you will see everywhere

Word	What it means
Gross pay	What an employee earns before anything is taken off: salary, hourly pay and overtime.
Net pay (take-home pay)	What is left after taxes and deductions. This is the amount that lands in the employee’s bank account.
Withholding	Tax you take out of an employee’s pay and send to the government on their behalf, such as federal and state income tax.
Employer taxes	Taxes you pay on top of wages, out of your own pocket: your half of Social Security and Medicare, federal unemployment tax (FUTA) and state unemployment tax (SUI).
FICA	Social Security and Medicare taxes. The employee pays one share, and you pay a matching share.
FUTA / SUI	Federal and state unemployment taxes. Only the employer pays these in most states.
Pay run	One payroll for one pay period, from calculation to payment.
Pay items	The building blocks of a payslip: salary, overtime, each tax. Bokapsys calls them pay components on the Compensation page.
Posting	Recording something in your books (the general ledger), so it shows up in your reports.

The Glossary has more.

What Payroll does for you

Keeps a record of your people. Each employee’s personal details, Social Security number (stored encrypted), work state, home address, pay rate, pay schedule and tax forms. See Employees.
Works out withholding. Federal income tax from each person’s Form W-4, Social Security and Medicare, state income tax for the states where Bokapsys holds the published tables, and state or local figures you enter yourself. See Withholding.
Works out employer taxes. Your share of Social Security and Medicare, FUTA, and state unemployment tax from the rate on your state’s notice.
Runs payroll. You create a pay run, Bokapsys calculates it, you check it, approve it and post it. See Run payroll.
Records payroll in your books. A posted pay run creates entries in your general ledger: wages and employer taxes as expenses, and the taxes and net pay you still owe as liabilities. Your Income Statement and Balance Sheet pick it up automatically. See Payroll in your books.
Produces payslips and a bank file. You download a payslip for each person, and a direct-deposit file you upload to your own bank. See Paying employees.
Feeds Tax. Posted pay runs are the figures behind your payroll tax deposits and your Forms 941, 940 and W-2. See Payroll filings and Deposits.

What Bokapsys does not do

Bokapsys does not send anything to the IRS, the Social Security Administration or any state, and it does not move money. It prepares the figures, the forms and the upload files. You pay your employees through your own bank, pay your taxes through the agency’s own service (for federal payroll tax, that is EFTPS), file your returns through the agency’s own website, and then record in Bokapsys how and when you did it.

Who can use Payroll

Payroll and Tax are included in every workspace, on every plan. You don’t need to ask for them to be switched on.

Payroll works with Tax. Several setup steps (your employer tax number, your state registrations, your deposit schedule) live in the Tax area, which is available alongside Payroll. See Tax overview.
A workspace can have Payroll switched off. Bokapsys can switch Payroll (or Tax) off for a particular workspace. If you don’t see a Payroll group in your sidebar and your role should include it, contact Bokapsys. See Contact.
AI help is a separate allowance. The AI features in Payroll, such as the anomaly check on the dashboard, use your plan’s AI allowance. The Free plan does not include AI help for payroll; everything else in Payroll works on Free. See Subscriptions.
Your role decides what you can do. Inside a workspace, what you see and can change depends on your role. By default, the Super admin, Admin and CFO roles can create, approve and post pay runs; other roles can only view them, or cannot see Payroll at all. Your workspace’s admin can change this. See Team and roles.

The Payroll group in the sidebar holds these pages:

Page	What you do there
Payroll Dashboard	The setup checklist, headline figures and your next pay run.
Run Payroll	Create, calculate, approve, post and pay pay runs.
People	Employees, contractors and new starters (the Employees, Contractors and Onboarding tabs).
Time & Leave	Hours worked, leave requests, holidays and shifts.
Compensation	Your library of pay items: the standard US set and your own earnings and deductions.
Benefits	Benefit plans, enrollments, retirement and HSA/FSA accounts. See Benefits.
Payments	Your company bank account and direct deposit files, paper checks, payment batches and garnishments.
Payroll Reports	Tax liability, payroll register, year-to-date, new hires, workers’ compensation and other reports. See Payroll reports.
Payroll Settings	Your pay schedules, workers’ compensation rates, and importing from a previous provider.

The Payroll Dashboard

Open Payroll → Payroll Dashboard. At the top is a card called Get started with Payroll, with a line such as “4 of 11 steps complete”. The card disappears once every step is done.

The New pay run button at the top of the page stays greyed out until the blocking steps of the checklist are done.

If any of your employees work in a state where Bokapsys does not hold the published withholding tables, an amber note says State income tax is not worked out for and names the states, with a Review employees link. See State coverage.

Below that you see four figures:

Tile	What it shows
YTD gross payroll	Total gross pay on posted and paid runs since 1 January this year.
Active employees	How many W-2 employees are active, and how many active contractors you have.
Pending runs	Pay runs that are still a draft, in review or waiting for approval. Needs attention shows when there are any, and a red count shows if any runs failed.
Open anomalies	Unusual figures flagged by the AI check in the last 30 days. All clear when there are none, Not checked yet before the first check.

And a Next pay run card with the run number, its status and its pay date (with Pay date has passed in red if it is overdue), or a prompt to create a run. Any runs that failed are listed underneath with an Open run link.

The readiness checklist, step by step

Each step in Get started with Payroll has a title, a one-line explanation and, when it is not done, a button that takes you to the place to fix it. The next step to do is highlighted. When something is wrong, a red line under the step tells you the consequence in plain words.

The steps fall into three kinds:

Blocking steps. Bokapsys cannot calculate a payroll until these are done.
Warnings. Payroll will calculate, but some tax or some year-end file will be wrong or missing. Fix these before your first real payroll.
Only if it applies. Marked “Only if it applies” in the checklist.

#	Step	Kind	Done when	What the red line means if it is not done	Button
1	Add your employees	Blocking	At least one employee is on file.	“No employees yet.”, or how many people have no work state, so no state tax is calculated for them.	Add employees
2	Set up pay items	Blocking	You have pay items (the standard US set is added in one click).	“Payroll cannot be calculated without the standard pay items.”	Set up pay items
3	Create a pay schedule	Blocking	At least one active pay schedule exists.	“No active pay schedule yet.”	Add schedule
4	Enter your employer tax number	Warning	Your full EIN is saved in Tax Setup.	Without it every W-2 and 1099 file will be refused in January.	Enter EIN
5	Record every employee tax number	Warning	Every current employee has a Social Security number on file.	Tells you how many people have no tax number. An SSN is required on each W-2.	Review people
6	Register for federal payroll tax	Warning	You have a federal payroll withholding registration in Tax Setup.	No federal registration, so no federal filings (941, 940) will be generated.	Register
7	Register in each state you employ people	Warning	Every work state your employees have is registered.	Names the states you are not registered in. Nothing will be withheld or charged there.	Register
8	Enter your unemployment rate and wage base	Warning	Each state unemployment registration has both a rate and a wage base.	Without them, unemployment tax is charged as zero.	Enter rate
9	Confirm your federal deposit schedule	Warning	You have told Bokapsys whether the IRS made you a monthly or semi-weekly depositor this year.	Bokapsys works it out from the payroll it can see, which is a guess until you confirm it.	Confirm schedule
10	Import year-to-date figures if you are switching provider	Only if it applies	You have posted at least one payroll in Bokapsys.	Skip it if this is your first payroll of the year. If you already paid people elsewhere this year, wage limits restart and too much tax is taken.	Import figures (opens Payroll Settings → Import from previous provider)
11	Run your first payroll	-	You have created at least one pay run.	-	Run payroll

Steps 4, 6, 7, 8 and 9 take you to pages in the Tax group. Set up payroll walks through every one of these in detail.

Your first payroll

1Company tax details
2Pay schedule
3Pay items
4Employees
5Registrations and rates
6First pay run

The order that avoids rework.

Before you start, gather:

Your EIN (Employer Identification Number), from IRS letter CP 575 or a past Form 941.
Your business’s legal name and address, exactly as the IRS has them.
Each employee’s completed Form W-4 (federal withholding) and any state withholding form.
Each employee’s Social Security number, home address, work state, hire date and pay rate.
Your state withholding and unemployment registration notices, which give your state account numbers, your unemployment (SUI) rate and the taxable wage base.
The IRS notice telling you whether you are a monthly or semi-weekly depositor (if you have one).
If you already ran payroll elsewhere this year: each person’s year-to-date totals from that provider.

Enter your company’s tax details. Go to Tax → Tax Setup → Taxpayers and add your business with its full EIN. See Set up payroll.
Create a pay schedule. Go to Payroll → Payroll Settings → Pay Schedules and click New schedule. See Pay schedules.
Add the standard pay items. Go to Payroll → Compensation → Components and click Set up US payroll. See Compensation.
Add your employees. Go to Payroll → People → Employees and click Add employee. Once the person is saved, fill in their W-4 on the same page. If you are moving from another provider, you can import employees from a file instead. See Employees and Switching providers.
Register with the IRS and your states. Go to Tax → Tax Setup → Jurisdictions and click Register jurisdiction for federal withholding, and for withholding and unemployment in each state. See Set up payroll.
Check the Payroll Dashboard. Every step should be ticked except Run your first payroll (and the switching-provider step, if it does not apply). Read any red lines and fix them.
Run payroll. Go to Payroll → Run Payroll, create a pay run, calculate it, read every warning, then approve and post it. See Run payroll.

The life of a pay run

1Draft
2Review
3Approved
4Posted
5Paid

A pay run moves through these statuses.

Status	What it means
Draft	Created but not yet calculated.
Review	Calculated. Check the figures and any warnings. You can recalculate as often as you like.
Approved	Someone with approval rights has signed it off. You can still recalculate or cancel it.
Posted	Recorded in your books. Its taxes now count toward your deposits and returns. A posted run can be reversed.
Paid	You recorded how and when everyone was paid. A paid run can no longer be reversed; fix mistakes with a correction run.
Cancelled	Set aside before it reached your books. Nobody is paid from it.
Reversed	Undone in your books after it was posted.

Run payroll covers each step.

How to check you are ready

The Get started with Payroll card shows no red lines except on steps that truly do not apply to you.
On People → Employees, every person you pay shows Active, a work state and a hire date. Someone hired with a future start date shows Not started yet and is left out of pay runs until then.
When you calculate your first pay run, read the amber card Some tax could not be worked out, if it appears. Anything listed there was left out rather than guessed, so it must be fixed before you file.

Common questions

I can’t see Payroll in the sidebar. Usually your role does not include Payroll, so ask your workspace admin. If the role is right and Payroll is still missing, it has been switched off for your workspace; contact Bokapsys.

A checklist button takes me to a “403” page. The step’s page is in the Tax area and your role cannot open it, or Tax has been switched off for your workspace. Ask your admin, or Bokapsys.

Can I run payroll for employees outside the US? No. Payroll in Bokapsys is US payroll.

Payroll in your books