How do I adjust synchronized invoice amounts for deposits that were reduced either by merchant services fees or were increased due to tips when reconcilling?

I can help you adjust the invoice amount, clean.

Le'ts record the invoice payment first in QuickBooks Online (QBO). Once done, deposit the invoice payment in the Bank Deposit page. Then, add a line item for Merchant fees (negative amount) and tips (positive amount) in the Add funds to this deposit table (as shown in the screenshot below). 

Here's how:

1. Click the Plus icon (+) on the Toolbar.
2. Under Other, select Bank Deposit.
3. In the Choose an account field, select the bank account to which to deposit funds.
4. Place a check mark on the invoice transaction to deposit in the Select the payments included in this deposit or QuickBooks Payments sections.
5. In the Add funds to this deposit table, add a line item for Merchant fees (negative amount) and tips (positive amount). You can consult your accountant on what posting account you need to use when setting up the additional line items.
6. Click Save and close or Save and new.

For more details about recording bank deposit, you can check out this article: https://quickbooks.intuit.com/community/Banking-and-bank-feeds/How-to-record-bank-deposits/m-p/18556...

That'll do it. Just add a comment below if you have more questions. Thanks!

Thank you very much! I think for any deposit generated from QB that will work swimmingly, however I am trying to match synchronized (via my credit union) Square deposits that are in the bank register, but cannot be matched to an invoice because the amounts differ. (see attached)

Thank you for getting back and giving more details, @clean.

I can help you resolve the amount difference to match your invoice in QuickBooks Online.

You're already on the correct page to match your transaction. Next thing you need to do is either adjust the transaction amount or select the Resolve Difference.

I'll show you how:

1. Since the total is more than the amount of the downloaded transaction, you can adjust the QuickBooks Online transaction amounts.
2. Put a check mark on the transaction.
3. Or, at the bottom, you can also select Resolve Difference to open the Add resolving transaction fields to enter a resolving transaction for the difference.
4. Select Save.

For detailed instruction, you can check this article: How to add and match downloaded banking transactions.

That should point you to the right track. Don't hesitate to ping me if there's anything else you need. Have a good one.