We use Cash Vat system, manually input opening balances on ledgers splitting out the VAT, only the net figure is on the ledger, how do I show the full payment coming in?

Glad to have you here on the Community page, @gareth.m.

In QuickBooks Online (QBO), only by using the VAT codes can be counted as VAT amount for the VAT return. And, only a VAT payment transaction type will be acknowledged by QBO as a payment on your VAT. Manually recording the VAT payment through the ledger will only appear on your reports but will not be reported on your VAT page.

For additional reference about VAT returns, skim through these articles:

• Submit a VAT return in QuickBooks Online
• Record a VAT payment or refund [Video]

Post again if you have any other questions. I'm always here to help. Have a good day!