Invoices and receive payments

Every time I send out an invoice and they pay me, I select received payment. Then I send the paid invoice to my client. However when I go through my quarterly earnings it is saying I made way more than I have. I go through and it looks like it is taking the total from the invoice and the receive payment as two separate transactions instead of the same one. Example: customer is invoiced for $450. They hand me a check of $450. I click receive payment and send the paid invoice on its way. But when I look on sales the invoice is complete and payment received are both the same. Didnt realize this was a problem until I looked at last years numbers and it said I made 65k but I only made 45k. It double a lot of my transactions. Can someone tell me how to stop this from happening again.