You can mark an invoice as paid by check or cash from the invoice tab:
Select the invoice you would like to mark as paid
If you are marking the invoice as paid by check, click the blue 'Record Payment' button.
In the box that pops up, indicate how much of the full payment you would like to mark as received
Select the form of payment you have received and include a memo you would like
Click 'Record $XXX Payment'
If the patient will be paying all of their membership dues by check, you can disable autopay on the payment option tab.