It’s nice to see new users here in the Community, jleigh37!
Thanks for elaborating the situation. You’re already on the right track; there are just some few steps we need to include in-between. I’ll be here to lend a hand.
When the earnings’ transactions are downloaded from your bank into QuickBooks Online, the default account used is Unrecognized Income. From there, the program already recognizes it as money-in type of deposits.
Your way of breaking out those customers’ services via invoices and marking them paid are correct. You only need to match those payments to the downloaded deposits to avoid duplicates.
I’ve added an article below for additional reference:
By doing these steps, you should now be able to manage those transactions without duplicates.
The Community is always here to help you with any QuickBooks concerns. Don’t hesitate to post here at any time and I’ll around.
Cheering you and your business to continued prosperity.