Hi,
A business must normally account for VAT on the VAT return for the tax period in which the tax point occurs, at the rate in force at that time.
But, if you use the Cash Accounting Scheme this may be different. For more information on the special rules for this scheme read Cash accounting (VAT Notice 731).
For guidance on tax points please refer to notice 700 section 14
Time of supply (tax point) rules
If your current system is not enabling you to be able to meet the VAT record keeping requirements, then that is something you would need to look at adjusting and whether there is a better electronic system your software provider may be able to assist you with.
Guidance on keeping VAT records and be found here:
Record keeping (VAT Notice 700/21)
Thank you.