Paying employees

Once a pay run is posted, your employees need their money and their payslips. Bokapsys moves no money. It builds a direct-deposit bank file that you upload to your own business bank, and your bank pays everyone. If you pay some people by check, you write the checks yourself and record their numbers in Bokapsys. Either way, you then record that the run was paid, and give each person a payslip PDF.

1. 1Post the pay run
2. 2Download bank file
3. 3Upload it to your bank
4. 4Bank pays employees
5. 5Record the payment

Words used on this page

Word	What it means
Direct deposit	Paying wages straight into an employee’s bank account.
ACH	The US bank network that carries direct deposits.
NACHA file (bank file)	A plain-text file in the standard format US banks accept for a batch of ACH payments. Bokapsys’s file ends in .ach.
Routing number	The 9-digit number that identifies a US bank. It is printed at the bottom left of a check.
Account number	The number of the employee’s account at that bank.
Garnishment	An amount a court or government agency orders you to take from an employee’s pay and send to someone else, such as child support.

Before you start

• The pay run is posted. See Run payroll.
• Each employee you pay by direct deposit has a bank account in Bokapsys (see the next section).
• Your own business bank offers ACH payroll uploads (“ACH origination”, “payroll direct deposit” or “batch payments”), and you know how to upload a file in your online banking. Your bank may need to set this up for you first.
• Your company bank account is set up in Bokapsys (see Your company bank account).
• Your role can manage payment batches. The bank file and Record payment buttons only show for roles that can.

Collect your employees’ bank details

There are two ways an employee’s bank account gets into Bokapsys:

• You enter it on the employee’s record, under Direct deposit → Add bank account. See Employees.
• The employee enters it themselves under Account → My Direct Deposit, if they have a Bokapsys sign-in. They can also split their pay between accounts. See Employee self-service.

How the details are protected. Full routing and account numbers are stored encrypted. Screens only ever show the last four digits. The full numbers are used only to write the bank file. Bokapsys checks every routing number before saving it, so a mistyped one is refused.

When an employee changes their bank details themselves, they get an email confirming it (showing only the last four digits), and the people in your workspace who manage payroll payments are notified.

How pay is split between accounts

An employee can send part of each paycheck to one account and the rest to another. In the bank file, Bokapsys pays:

1. every account set to a fixed amount each payday, then
2. every account set to a percentage of pay (a percentage of net pay), then
3. whatever is left to the main account.

The payments for one person always add up to exactly their net pay. If the fixed amounts and percentages would come to more than their net pay, the later ones get less and the main account gets nothing.

Example: Jo’s net pay is $1,500.00. Jo sends $200.00 to savings and 10% to a second checking account. The file pays $200.00 to savings, $150.00 to the second account and $1,150.00 to Jo’s main account.

Your company bank account

The bank file has to name the bank account the money leaves from and your company’s ID with that bank. You set this up once.

1. Open Payroll → Payments. The Direct Deposit tab opens.
2. Under Company bank account, click Add bank account. The Company bank account window opens.
3. Fill in the fields below and click Save. You see Bank account saved, and the account shows In use.

Field	What it means	Required?	Example
Bank name	The name of your bank.	Yes	First Ohio Bank
Routing number	Your bank’s 9-digit routing number.	Yes	041000124
Company name on statements	How your company’s name appears on your employees’ bank statements. Up to 16 characters.	Yes	MAPLE ST BAKERY
Payment description	The short description employees see. Up to 10 characters. Defaults to PAYROLL.	No	PAYROLL
Company ID	The ID your bank gave you for ACH. Leave blank to use 1 followed by your EIN, which is what most banks expect.	No	1123456789

To change it, click the pencil icon on its row. To stop using it, click the stop icon; new bank files are then not built from it.

Download the bank file

You can download the file from the pay run, or from Payroll → Payments → Direct Deposit.

1. Open Payroll → Run Payroll and click the posted run’s number.
2. Click Download bank file. A window titled Direct deposit file opens and checks the run.
3. Read the summary: Payments in the file, the Total, the date your bank will pay, and two lists: In the file (each person and amount) and Not in the file (each person left out, and why).
4. Click Download. Your browser saves a file named like direct-deposit-PR-00001.ach.
5. Sign in to your business bank and upload the file in its ACH or payroll upload screen. Follow your bank’s instructions to approve the batch.
6. Pay anyone listed under Not in the file another way.
7. Once your bank confirms the payments, go back to the run and click Record payment, choosing Direct deposit file. See Run payroll.

On Payroll → Payments → Direct Deposit, the Posted pay runs list has a Bank file button on each posted or paid run. Its window also shows which account ending each person is paid to, and warns you if the run is already recorded as paid (“Uploading this file again would pay these people a second time”). Bank files made lists every file Bokapsys has built, with the pay run, date, number of payments, total and the account it is paid from.

What is in the file

• One batch of credits (money going to your employees), with your company name and payment description.
• One payment per account, per employee, for their share of net pay, to their checking or savings account.
• Each payment carries the employee’s name.
• The effective date is the day you are asking the bank to deliver the money. It is the run’s pay date, moved to the next banking day if the pay date is a weekend or bank holiday. If the pay date is too soon or has passed, the file asks for the earliest day your bank can pay, and the window warns you that employees will be paid late.

Who is left out of the file

Reason shown	What happens
No bank details on file	The employee has no bank account in Bokapsys.
Routing number is not valid	The routing number on file doesn’t pass the bank check.
Nothing to pay this run	Their net pay is zero.
Already paid another way	They were already recorded as paid by check or by hand on this run.

Only that person is left out. If nobody on the run can be paid, no file is built and the window explains why.

Worked example

Run PR-00001 pays three people:

Employee	Net pay	Bank details	In the file?
Maria Lopez	$1,690.85	Checking, main	Yes, $1,690.85
Sam Patel	$1,240.10	Savings $100.00, checking for the rest	Yes, $100.00 and $1,140.10
Jo Kim	$980.00	none yet	No: No bank details on file

The downloaded file contains three payments totalling $2,930.95. You pay Jo $980.00 another way, and ask Jo to add a bank account before the next payroll. When you record the run’s payment as Direct deposit file, Maria and Sam are recorded as paid by direct deposit and Jo as paid outside Bokapsys.

Paper checks

Bokapsys does not print paychecks. You write them from your own checkbook and record each one in Bokapsys, so you can see which checks have cleared your bank.

1. On the posted pay run, click Record payment and choose Checks in How you paid.
2. Open Payroll → Payments → Checks. Each paycheck without a number is listed under Checks to record, with the payee, pay run, pay date and amount.
3. Click Record check on a row. Enter the Check number printed on the check and the Date on the check, and click Record check. The check moves to Checks written with the status Not cleared yet.
4. When the check appears on your bank statement, click the tick icon (Mark as cleared), enter the Cleared on date and click Mark as cleared.

Voiding a check. If a check is lost or wrong, click the void icon, give a Reason and click Void check. The check shows Voided, and the same payment reappears under Checks to record with Record replacement, so you can record the new check. Voiding a check does not change your books, because the payment itself still stands.

Payment records

Payroll → Payments → Payment Batches lists one row per pay run you recorded as paid:

Column	Meaning
Pay run	The run, with a link to it.
Pay date	The run’s pay date.
Payments	How many payments were recorded.
How	For example “3 direct deposit, 1 check”.
Total paid	The total of the payments.
Matches net pay	Yes when the total equals the run’s net pay; otherwise it shows the net pay so you can see the gap.
Problems	Any payments returned by the bank or failed.

Click the list icon on a row to see each payment: who was paid, the method, the amount, the reference (check number or trace number) and its status.

Payslips

A payslip (pay stub) is created for each employee when you post a run.

1. Open the posted run. Under Pay and payslips, each employee has a PDF button.
2. Click PDF next to a person. Your browser saves their payslip.

Employees with a Bokapsys sign-in can also see and download their own payslips from Account → My Payslips.

What a payslip shows

Part	Content
Header	Payslip, your logo and brand colour, and your business’s legal name.
Employee	Name, ID (employee number) and Work location (work state and country).
Pay period	Period start and end, and Pay date.
Employer details	Your legal name, address and phone, from your primary taxpayer in Tax Setup (or from Company settings if there is none).
Earnings	Each earning, with hours and rate for hourly lines and the kinds of hours paid.
Employee taxes	Federal, Social Security, Medicare, state and local tax.
Deductions	Benefits, retirement, HSA/FSA, your own deductions and garnishments.
Employer costs (not taken from your pay)	The taxes and contributions you pay on top, shown for information.
Totals	Gross pay, Taxes and deductions and Net pay.

Every line has two amounts: Current (this paycheck) and Year to date (everything paid through Bokapsys in the calendar year up to and including this pay date).

What a payslip does not show

Some states require more on a pay statement than Bokapsys prints. Check your state’s rules and give employees the missing information another way if needed. In particular, the payslip does not show:

• a paid sick leave balance (California requires one),
• a separate overtime rate line (New York requires one),
• amounts paid by a previous payroll provider earlier in the year: its year-to-date column covers pay through Bokapsys only.

A payslip is a fixed record of the posted run. It does not change if you edit the employee later. If the run is reversed, its payslips are voided.

Garnishments

A garnishment order tells you to take money from an employee’s pay. Add each order once and Bokapsys takes it off every pay run.

1. Open Payroll → Payments → Garnishments.
2. Click Add garnishment. A window titled Add garnishment order opens.
3. Fill in the fields below and click Save. You see Garnishment order added and the order appears with the status Active.

Field	What it means	Required?	Example
Employee	Who the order is for.	Yes	Maria Lopez
Type	Child support, Spousal support, Federal tax levy, State tax levy, Student loan, Creditor, Bankruptcy, Wage assignment or Other.	Yes	Child support
Order number	The case or order reference.	No	CS-2026-0412
The order includes arrears	For support orders: tick if the order covers support more than 12 weeks overdue.	No	Unticked
The employee supports another spouse or child not covered by this order	For support orders: tick if this applies.	No	Ticked
Send payments to	Who you send the money to.	Yes	State Disbursement Unit
Amount each pay period	A fixed dollar amount each pay.	One of these two	150.00
Or % of disposable pay	A percentage of disposable pay (pay after taxes).	One of these two	20
Total balance owed	The total the order covers.	No	3,600.00

How much can be taken

Federal law limits how much of an employee’s disposable pay (pay after taxes) a garnishment can take, and the window shows the limit for the type you choose:

Type	Most that can be taken
Child or spousal support	60% of disposable pay, or 50% if the employee supports another spouse or child. Plus 5% when the order includes arrears (so up to 65% or 55%).
Federal student loan	15% of disposable pay.
Creditor, wage assignment and other	25% of disposable pay, and never more than the amount above 30 times the federal minimum wage per week, after any higher-priority orders.
Tax levies	The amount on the levy notice, up to what is left of disposable pay.

Several orders are taken in priority order, each within its limit. The support order flags matter: an order without them is limited to the 60% figure.

Caution

Bokapsys withholds the money but does not send it anywhere. You pay the agency or person named in the order yourself. Orders can’t be edited or ended on this page, so keep track of what has been paid, and contact Bokapsys support when an order is satisfied or changes.

Related

Run payrollCreate, calculate, approve, post and record payment.

Payroll in your booksWhat posting and paying record in your ledger.

Employee self-serviceHow employees add bank details and see payslips.

Security overviewHow Bokapsys protects sensitive data.