Hello @sarahtyrer, welcome to the Seller Community! 

If you want to mark an invoice as paid, this action can be done from the Square Dashboard. Just head to the invoices tab on the left side of the screen. Click on one of your unpaid or overdue invoices. This will open a new window with invoice details. In the top right corner click on more. This will give you the action to mark the invoice as paid. 

Please let me know if you need help with anything else! 😀