In order for bank reconciliations go smoothly, it is important to record customer payments properly in QuickBooks. To do this, transactions in your QuickBooks check register need to match how they appear on the bank statement.
When you go to the bank and deposit several customer payments using one paper deposit slip, the bank statement will show the payments as one lump sum. In QuickBooks, your checking account register should show the one lump sum as well, even though the payments may be from different customers and received at different times.
If you have issued an invoice to a customer, and the customer then later pays it, here is how to record the customer's payment: