Client will sometimes pay outside of Bonsai, such as through check, cash, or wire transfer. That's ok! You can still manually mark your invoices as paid.
After you've sent an invoice to a client or created a link for it ( http://intercom.help/bonsai/bonsai-for-freelancers/how-can-i-send-my-invoices-as-a-url), just go to the invoice, click on the 'More options' tab, and then click on 'Mark as paid'.