I appreciate your elaboration regarding the amount difference on the stub and check, thewinecountry. I'll explain in detail below how direct deposit works in the system.
When you transmit Direct Deposit payroll to Intuit, QuickBooks automatically creates a Payroll Liability check that you can find in your bank register. You don't have to manually mark each deposit as cleared, as QuickBooks does it for you.
The checks show $0 in the register window to avoid duplicating the debit amount included on the QuickBooks Payroll Service Liability. Doing so will make the Direct Deposit paychecks $0, allowing QuickBooks to recognize this as a cleared transaction.
Otherwise, check out this article if you can't find the Direct Deposit Liability check: Recreate a missing or voided direct deposit paycheck in QuickBooks Desktop Payroll.
If it's the first time for your employee to receive pay via direct deposit, you'll need to set up them first then use this reference to process payroll on time: Send direct deposit paychecks in QuickBooks Desktop Payroll.
Once done, visit this guide to determine the direct deposit lead time and when to submit payroll: When to send your direct deposit payroll.
Furthermore, this module will aid you in generating reports to see the amounts and balances: Run payroll reports.
Keep me posted if you have other questions about processing payroll via direct deposit. I'm always here to help. Stay safe.
