Hi @Peter
As long as you have one copy of an invoice to present to the customer with the required information (required by HMRC), then there would be no need to issue a second invoice.
If you anticipate a lot of sales, you can just log them daily/weekly under a generic customer name. Check this article out:
http://community.quickfile.co.uk/t/accounting-for-daily-takings/8911
If the site is being built for you, you may want to ask your developer to take a look at our API. This could save you quite a bit of work too 