I have had two customers with this issue. They sign up with QBO payroll (Full Service or Enhanced). They click the workers tab, follow the instructions to get going with Payroll and link their payroll bank acct. They see the debit and verify it. All good, right? Well not always. It never sends you to gear>payroll settings>accounting>bank acct. to select the actual account for the entry of the payroll check tranactions.
By default, QBO grabs your top bank account. For my latest customer, that was his Savings account. Whoops! You notice (after payroll is processed) that the paychecks are in the wrong bank acct. in QuickBooks yet they cleared the correct bank account at the bank level.
The fix (and it is a bit ugly) is to create transfers from the bank acct. that the checks did clear from to the bank acct. that QBO new payroll settings put them in. I called payroll support on the first client this happened with and was told "there is no way to change the paycheck bank account once it is entered into QBO". Even they cannot change it. Watch the video for a live view of the "fix". Here is the blog post that goes with the video. Enjoy!