Can I mark an invoice as paid?

You can mark an invoice as paid by going to Contacts > Client Name > Invoices section (scroll down on the right side) > link 'View all' to get to the list of invoices.

Click on "View" from the drop down list to the right of the invoice, then scroll down (use the down/up arrows keys) and click on the button "Add payment".

Select the method of payment, reference value, adjust the amount (if it's a partial payment), then click the 'Update' button at the bottom. Once the invoice marked as paid, you can send the receipt via email to the client from the "Email to client" button at the bottom of the paid invoice.