If you backdate your VAT registration, you will need to issue a VAT only catch up invoice to your agency for the VAT from the period between your registration date, and the point were you start adding VAT. 

You can do this on one invoice, and we have a template you can use if you need it.

This invoice then needs to be added to your bookkeeping software in the month you issue it, along with your normal fees for that month. So for example if you issue a VAT only invoice in April for £5000, and your normal April fees come to £3000 + VAT, the amount you should enter in the April column of your bookkeeping software, is £8,600.