Just another post to say this feature is messed up.  2 years of people saying "WTF" and it's still wrong without a proper way to fix it, just a workaround.

My accounting was set to the wrong bank account (of the 3 setup).  I agree with the others that say, there's no reason the tool couldn't easily figure out the right bank account for transactions when you setup the payment account.  No good reason for it to be in two places.

Furthermore, there never seems to be a way to fix transactions with payroll.  The workaround is always "make a journal entry".  I guess the Payroll team is okay with not allowing people to fix mistakes.

Multiple occasions now I've thought "wish I had picked an external payroll provider", that way I could fix things in QB when it goes wrong.