QuickBooks Point of Sale & QuickBooks Enterprise

If you don’t see any payments on this list, but you do see invoices that you know have been paid, it’s likely that they were deposited into the bank without going through Receive Payments first. You’ll need to find the deposits and change the account to Accounts Receivable and enter the Customer name.  Once you do this, they’ll show up on the Open Invoices report and you can apply the credits as explained above.

It’s always best to use QuickBooks the way it’s designed. If you enter invoices, you should always use Receive Payment.  Never go directly to Make Deposit or enter the deposit directly into the register. If you don’t enter invoices, you should use Enter Sales Receipts so you can batch the payments using undeposited funds (see below).  

It’s also a good idea to deposit your payments into undeposited funds, and then enter the deposit on the day you’re actually going to the bank.  When you select Make Deposits, a popup box will list all the payments you’ve received into undeposited funds that haven’t been deposited yet.  Simply select the payments that you are depositing that day, and Quickbooks will batch them all in one deposit that will match your bank statement.