Hello!
This is a great question. It's awesome to hear that you're working both with Payroll direct deposit and the banking feeds in QuickBooks online. Both of these offer the opportunity to speed up the process of working with your data in the program, but I can see how a situation like the original poster is asking about, where the employee payroll is set to go into two bank accounts, might complicate matters. I can explain how this works.
When you run payroll by direct deposit in QuickBooks Online, the program should be creating a single transaction in the books as well as creating a single payment transaction for the same entry in your bank account despite it being paid to two different accounts. In those instances, you can just match the transaction in the bank feed because it's a match of one-to-one, which Payroll transactions want for this feature.
If for whatever reason your bank has it split into two transactions, I recommend excluding them from the feed and manually reconciling the transactions later when you go through the reconciliation process. Excluding the transactions doesn't hurt your books; it quite literally means you'll need to manually reconcile later, like I mentioned. Here are some articles on excluding and reconciling for you.
I hope this has helped! If you have further questions, don't hesitate to reply on this thread again.
Enjoy your day!
