Manual Payments and Importing Bank Statement Conflict

I hope someone can shed some light on this for me, because how I see it, when I accept manual payments, I will eventually create a duplicate when I import the bank statement.

Here's what I'm doing: I go about my business performing work and invoicing customers as usual. When I receive a check in the mail, I go into the corresponding invoice and mark it as paid by adding a manual payment. That way I can track the date the invoice is paid and the invoice is shown in the right state in my list. I may not deposit that check in the bank for a few days or even a week. I also only download my bank statement about once or twice a month. The problem comes when I import a new bank statement after that check was deposited with other checks. I can't associate part of that deposit with the invoice because I already marked that invoice paid. If I did, the account would have two duplicate payments. I don't want to wait until I import the statement to then mark the invoice paid because the status of the account wouldn't be accurate in my dashboard.

How am I supposed to be doing this?