Let's link the deposits to the invoice, Jmp17.

I'll show how to do it:

1. Open the Invoice, then click Receive Payments.
2. In the Customer Payment window, select Apply Credits.
3. Put a check mark in the box beside the Date of the invoice.
4. Then, click Done.

I've added screenshot as reference:

Let me know how these steps works. I'll be here if you need more help.