What you need to use is an intermediate holding account. Set up an account and call it something like Checks Received or Undeposited Payments. Then enter the payments into it. Then when you make the deposit to your bank account you transfer the total deposit amount to the new account. That way when you download your bank transactions the deposit will match. Or you should use the holding account if you receive payments in one year (like in Dec) but don't make the deposit until the next year (like Jan.).
You don't run to the bank each time you get a check. So you need a holding account so you can show the income when you received it. Then you wait until you get a bunch of checks to go to the bank.