Hi there, becmossman.
To sort the issue about the discrepancy of the pay run amount to the employees bank account, I suggest doing a manual find Match and use the Resolve Difference option. This way, you'll be able to add a new transaction to match the correct amount.
Here's how:
1. Click Banking at the left panel. Then Banking section,
2. Find and select the transaction in the For Review tab.
3. Choose Find Match radio button.
4. From the Match transactions window, select the checkbox of the appropriate transaction.
5. Choose Resolve Difference to open the Add resolving transactions fields.
6. Click the Add new transaction button.
7. Select a category.
8. Enter the amount which is the few cents.
9. Hit the Save and close button.
Please check this article on how you can easily add and match journal entry to transactions from your online bank account: Matching payroll payments in QuickBooks Online.
Please know that you're always welcome to post if you have any other concerns. Wishing you and your business continued success.
