Paying an Employee from 2 Separate Bank Accounts in Quickbooks Desktop 2022

Joining you here to help with your payroll-related questions, Nicki5.

QuickBooks gives you an option to manually edit or change the number of hours when creating two paychecks. I'd be glad to share these steps with you:

1. Go back to the Payroll Center and click Start Unscheduled Payroll.
2. Open the Preview Paycheck window.
3. Make sure that the Pay Period dates are accurate so the system would save the remaining hours in creating the second paycheck.
4. Proceed to the Hours column and manually change or type in the number of hours. 
5. Click Save and close. 

You can read more details about this here: Create Paychecks Based on Timesheet Hours.

Additional details and guidance when running payroll are also discussed in these articles:

• Reduce Paycheck Wages for an Employee Who has Been Overpaid
• Create a Total Hours Worked by Employee Report

Don't hesitate to post your follow-up questions in your reply. We'll make sure that everything is sorted out. 

Thank you for your answer! Will that delete the other hours in the system and mess up my payroll taxes, or will that add to my payroll taxes and keep all hours logged somewhere in Quickbooks?

@Nicki5  RE: How can I cut 2 separate paychecks in Quickbooks Desktop Pro Plus? 

Creating two separate regular paychecks for one pay period (as compared to say, a special bonus check) is not a good idea, because it'll have the effect of significantly reducing the Federal and State withholding tax for the period when the tax on both checks is added together. Which is bad.

The best way to do this is to create and use a net deduction payroll item that is set up using a holding account, probably a liability account set up for this purpose. Add it to the paycheck and enter the $ amount for the other account's check. After recording the paycheck, then add a regular check to the other bank account for the same amount using the same holding account.

Then print both checks, where one has all of the payroll details and the other is just a standard check.