Hi there, jd34mx.
After reading over your thread, I was able to figure out what seems to be going on. Payments made to you via Merchant Services don't require a deposit because they're auto-assigned. Below I'm including a helpful link that breaks down Payments made through the Merchant Service Center and much more helpful information.
I'm also including some helpful information on undeposited funds and how to utilize them. I would recommend reaching out to an accountant regarding the deposits you already have in place to see how you should handle them. If you don't have one yet, I highly recommend a ProAdvisor, they know all the ins-and-outs of the QuickBooks Product and are certified accountants.
If you have any other questions or concerns, feel free to post below anytime. Thank you and have a nice afternoon.
