Hi Lee
So what about the following as a solution:
1. When the money comes in from the customer click on 'split payment'
2. On the first line enter in your customer details, select the category 'debtors' and 'NO VAT' as the tax code. Enter in the amount you wish to allocate against the sales invoice
3. On the second line enter in your supplier details, select the category 'creditors' and 'NO VAT' as the tax code. Enter in the amount you wish to allocate against the supplier invoice. **This will be a minus figure**.
The split transaction should now balance and you can post it
4. Then you can allocate the supplier payment against the invoice it relates by raising an expense and adding the two transactions from the right hand side
5. The sales invoice and receipt can be allocated by using 'receive payment'
As a result your banking will be dealt with and the supplier and customer invoices will have the correct values allocated against them.
Hope this helps!
