Thank you for posting here in the Community, @parsonslawnservi.
I can share some clarifications about processing payments in QuickBooks Online. Right now, QuickBooks will only record deposits automatically if the system recognizes a matching sales receipt or invoice.
If your customers aren't reflecting on the deposited transaction, you'll need to match them manually. By doing so, you'll be able to keep track of the funds in a more detailed way.
For additional reference, I've attached some articles you can use for more insights about QuickBooks Payments:
Please know that I'm just a post away if you have any other questions. Have a great day ahead.