Clicking the Invoice button will show a screen much like the one below;
Fig 1 - "Invoice" button.
Fig 2 - Invoice
You can do the invoice at whatever intervals you deem appropriate. You could do one invoice for each treatment or wait and invoice for 3, 4, 5 etc. It may be better to wait and submit more treatments on a single invoice as this can reduce some of the admin time further.
The important aspect here is that you set the correct Reference. At the moment you will still need to activate the appointment as you normally would in TM2/TM3. That is, Complete, Create the Billing Item and then Invoice. In the future, this process will be handled by the booking in Pronto Bookings. The reference you use/is generated by this process is best used once again on the submission via Pronto so that you may easily find where the payment belongs.
You cannot adjust the invoice once submitted unless in the case of a Rejection.
If you don't do this it will develop like the example below;
Invoice in TM2/TM3 (normal creation) has a reference of 100. The submission via Pronto has a reference of 200. The payment that is sent will be for reference 200. When you come to reconcile the payment via TM2/TM3 you may not be able to find reference 200.