I have just started using Quickbooks Online in order to comply with Making Tax Digital for my VAT returns. I am a small Limited Company and am not on the Flat Rate Scheme.
I subcontract to a larger company, and invoice weekly. However there were various hiccups with their accounting during this quarter, and so I have a lot of Sales income that is made up of either:
a) Nett invoice amount with no VAT
b) Nett invoice amount, with VAT from the previous week
c) Correct invoice amount with both Nett charge and VAT
d) VAT only to correct missed payment
I'm struggling to find out how I properly code this Sales income so that my VAT return correctly reflects the actual situation. Up until now I've kept my own spreadsheets for VAT, made my own return online and then everything is run through my accountant at the year's end.
I am not a quickbooks expert, but would suggest that the issue isn't a quickbooks one but an invoicing issue from the company you are invoicing. As long as the invoices you are raising through quickbooks are correct - i.e. raise the invoice at standard VAT of 20%, then when the payments come in from your client match them off against your invoices. From what you described in your note, the payments from your client will not perfectly match your invoices, but that is OK as you can part match payments against invoices...and as long as they have paid you everything they owe you then it should also balance out.