Hi Leah, I stumbled across your query while looking for the answer myself. I contacted customer support and they said...
'The Invoices toll is designed to be used to charge clients custom amounts through the linked payment processor although Invoices aren’t connected to specific appointments.
If you want the these payments to be reported within your Sales reporting through your payment processor you can manually update the completed appointment as paid in cash and complete the sale. Consider adding a note that the payment came via cash or bank transfer and delete the unpaid invoice.'
I asked if this might be an option going forward and they said if enough people request it, then it probably would in the future. So keep letting them know :-)