Pay your merchant's fees invoices (Bank Supplier Payment) the same day as you receive the money; that way the two items on the bank rec will equate to the actual money received. But that would mean you'd have to hang on to the Merchant receipt until the charges were processed.

There may be a better way of doing this but we dont take card payments normally so avoid the hassle.

We have something similar but not with a credit card merchant.

Using your example we would post the full £1000.00 receipt against the customer invoice.

Then raise a supplier payment for £25.00 against the merchant at the same time. This then sits on the supplier account until the invoice is received.

Post the invoice to the supplier account and this then can then be matched to the payments using the supplier payment screen.

Hope this helps.

Thanks everyone - yes i did think about it for a day then came up with the same as you have both suggested - had seen on a previous thread about it they put the payment received against the customer invoice and put the shortfall down as a discount - which seem completely wrong to me - as merchant invoice is not getting aid off