There are a variety of methods for receiving payments from customers or one-time receipts. If you have submitted an invoice to the customer, then you will want to Receive Payment (found on the home page or under the Customers menu). If the client sends you money before you have invoiced them, you can create a Sales Receipt (also under the Customer menu). If you are going to be receiving installment payments or a deposit, then you will want to create a payment item for each situation. Finally, you can go to the Banking menu, select Make deposit and simply record the check information and deposit the funds into the proper bank account at the same time.
For more detailed information on receiving payments, go to mlkjoller.com for an extended article.