Applying an Invoice Against a Deposit

Hello all,I've been using QB for a few years now but it still confuses me. I invoice in a different program so I can have control of the design. So I decided that I wanted to make duplicare "dummy" invoices in QB so I can track my accounts due. So I am going back and retroactively creating invoices and want to apply payments but as I always simply deposit checks into one of my accounts, when I direct the invoice received to that account it of course shows up as two seperate deposits - one from the invoice payment received and one from the actual deposit. The deposit is attributed to "Income" and the invoice to "Accounts Receivable".What I'd like to do is create invoices and when I deposit a check say this "check X applies to invoice Y." Can I do this and how? Thanks!