What do I do with Counter Deposits if I've received my invoices into my bank account already?

Hi there, @Megamedia.

If you're referring to the deposits or payments you entered in the bank, and you want to match them to the downloaded transaction (counter deposit), you can accept this matched transaction on the For Review tab. 

Let me show you how:

1. On the Banking page, select the For Review tab.
2. If one match was found, the matching transaction appears in the Category or Match column.
3. If the match is correct, from the Action column, select Match to accept it.
4. The transactions you matched are moved from the For Review tab to the In QuickBooks tab and marked as matched.

However, if you receive a deposit from customers before services are performed, you can create a retainer in QuickBooks Online. I recommend the following article as it walks you through all the steps of the process, such as setting up a liability account, retainer item, and a liability bank account if necessary: How to record a retainer or deposit.

For additional reference, I've attached some articles you can use to manage downloaded transactions and to learn more about bank deposits in QuickBooks: 

• What are Bank Deposits in QuickBooks?

• How to add and match downloaded banking transactions

If you're referring to something else, please let me know by clicking the Reply button below. Additional details or screenshots of the problem will help us narrow things down. Have a great day ahead.