I'll give my advice, but I cannot say for sure if it's accurate tax wise for the UK.
If I have a project, and all my objectives in a row, I bill the full amount, then send out invoices with just a "memo" field on them. This way, my invoice program does not think I should be bringing in much more money, and I still have a record of what I have taken in and what is still left owing.
- Generate the Master Invoice. This invoice should have the final cost, including any and all parts, expected to be used and billed. This is the master amount you need to keep track of, on this specific invoice. In the memo field, include information about when you expect payments (i.e. 25% due January 15th, 2015; 25% due February 15th; remainder due March 15th; late fee of 2% per month for outstanding balances).
This will create the single reference, and ensure that the customer understand when/what he's being billed. You send this out, and save a paper copy for yourself.
Send out the next notice. This will be an invoice, but you will not have any chargeable items (except possibly the late fee). It will contain a memo field that states how much is owing, and how much has been paid already. It would be awesome if your program also allows you to apply previous payments into an invoice; each program is different though. The point is, you do not want to add new billings (unless required) to the original invoice.
Track payments on the Master Invoice. Remember how I said print it out for yourself as well? Use a pen, and write in any payments made towards that invoice, including the new balance owing. Mark when you send out a new invoice with the new total, then write a single line through each note about payments, so you always have a fresh copy.
Once the invoice is paid in full, you are done. Ensure the customer's account is at a $0 balance, and send a final thank you invoice/notice, explaining everything has been paid up.