Manual Credit Card Deposit Entry

We had our company file being worked on by our accountant and accidently ran our data transfer from the Quickbooks Point of Sale to Quickbooks Financial. This caused some work done to not be captured when the company file was restored. My accountant explained that everything missed would have to be manually entered. The first entry I did was for credit card sales for that day. I went to "record deposits" and selected what credit card payments were there from that day and then manually entered on the following lines the remaining payments received, but this didn't apply it to customer's with accounts. I was not able to use the account "undeposited funds" so instead used "merchandise sales" so I am not sure if that is why I cannot apply it to a customer account. They have paid but it is not recorded correctly. Is there a different way to record the payment so that I can apply it to the customer's account/sale? Would it be separate from the payments that got recorded correctly? Is there a better way to do manual entries for a mistake like this?