I think what you doing is correct to issue a proforma invoice, [which is legally binding], according to the articles: http://en.wikipedia.org/wiki/Pro_forma.

Mike C advise is good:
If one is going to use a Proforma Invoice, I think that when the payment is made, a Tax Invoice for the SAME DATE should be made out and sent immediately so that records can be kept clean. Alternatively an entry on the Tax Invoice stating that it replaces Proforma Invoice No: 123 would be a big help.
I also need to capture this document and can not capture a pro-forma invoice.
Pretty sure your accounting software can be adjusted to include this, what software are you using?