Invoices & payments

Hello, 

Here's a question that I can not seem to get a straight answer on and I am in desperate need of some help. 

I use my quickbooks online mainly for my payroll and to keep my banking synced with all my records. I recently decided that I wanted to keep all of my customers and invoices logged into my quickbooks to eliminate all the paper stacking up on my desk. I figured out how to do all that, but here's my problem. When they are paid obviously all of those checks get deposited into my account and synced to my quickbooks register. So when I go into receive a payment on the invoices, how can I make it so that it doesn't go into my bank account as accounts receivable? That just makes it so that my income is doubled if that makes sense? I just want to somehow mark that they are paid for my own personal reference. So basically I am just logging all of these invoices & payments for my own personal reference trying to avoid all the paperwork.