There is the standard workflow when prepayments are used:

1) Create and send a Proforma Invoice.

2) Receive and add a payment for the Proforma Invoice (as bank reconciliation or manually). -> Proforma is paid at this step

3) Create a final Sales Invoice by clicking on the Create a New Sales Invoice* button at the bottom of the Proforma Invoice form or just create a new Sales Invoice from scratch. It depends on do you need to copy the content of the proforma into the invoice or you don't.

*Save as Draft option will create a new invoice. You can offset such invoice later by clicking on the "Add a Payment" button and going to the "Use Prepayment" tab. 
**Post/Use Prepayment option will create, post and offset the invoice in one click.

4) Post the Sales Invoice

5) Add a payment to the Sales Invoice by offsetting it to the paid Proforma Invoice. It can be achieved by clicking on the "Add a Payment" button and then selecting "Use Prepayment" tab. -> If the invoice amount is equal to proforma amount then both documents are paid at this step

3-5 steps can be repeated if there should be multiple invoices for the same proforma invoice
5 step can be repeated if there should be multiple proforma invoices for the same invoice.
Links to all offset invoices are available from the "Invoices" tab of the proforma.
Links to all used prepayments are available from the "Payments" tab of the invoice.

There is also a special Proforma Summary report that shows due, paid and available amounts for every active proforma.