When you receive a check that pays a customer invoice, you can go to that
invoice and click on the button *Register Payment* and select the
*Check Received* journal as *Payment Journal*.

When you want to deposit checks to the bank, go to the menu
*Invoicing > Accounting > Check Deposit*, create a new check deposit and set the
journal *Checks Received* and select the bank account on which you want to
credit the checks. Then click on *Add a line* to select the checks you want to
deposit at the bank. Eventually, validate the deposit and print the report
(you probably want to customize this report).
