Direct Deposit

@ajpatrick  I am assuming you have two separate physical locations for your business.

I don't know if you do some employees' paychecks through direct deposit and some through physical checks, but the answer is the same in either case.

Run the direct deposit out of a single bank account and, as necessary, move money from the second bank account to reimburse for their share of the payroll.

How this is calculated can vary by specific company, but in general terms, you would multiply the number of employees at the second bank account by the direct deposit fee per employee. Then, you would add the result to the total Gross Wages and the total Employer Taxes and Contributions. Both of these can be found on the appropriately dated Payroll Summary filtered by the appropriate Class.

The final result will include the direct deposit fee, wages, and payroll taxes the second location is responsible for for that specific direct deposit.

Thanks for posting your concern in the QuickBooks Community page, @ajpatrick. Let me share some information about using the Direct Deposit feature in QuickBooks.

When you first set up payroll for direct deposit, you can only connect one bank account for you company. That means you can only pay employees through direct deposit from that account. 

However, you can pay employees with regular checks from your second bank account. As FishingForAnswers suggested, you can alternate between accounts when paying employees. You can also transfer funds from the second bank account and reimburse it.

Alternatively, consider using a third-party app that allows direct deposit from multiple accounts. You can search for such apps here: https://desktop.apps.com/home

Additionally, you can run payroll reports in QuickBooks to view helpful information about your payroll and employees.

Please add a reply if you have any other questions. I'm happy to help explain how to manage direct deposit across two accounts.

Working on this to see if I can get it changed. But I think it is going to work for me. Thank you.