To match up a payment on account with an invoice go to Bank - Customer - choose the relevant customer and then in the receipt column click on Pay in full against both the Invoice and the payment on account, after which the analysis total at the bottom of the window should be zero and then click on Save.
Another query.... What if the payment on account exceeds the invoice amount or vice versa. It does tell you to deduct the additional amount but where from?
Deduct the additional amount from whichever is greater, so that the amount being allocated is the same for the payment/receipt (it's the same principle in the sales and purchase ledgers) and the invoice.
In other words, if you have a payment for £11 and an invoice for £10, and you've clicked "Pay in full" or pressed for both items, change the payment amount so that it's £10 (you are allocating £10 of the payment against the invoice for that amount).
Since you are simply allocating something, rather than entering a new payment or receipt, you should ensure the total amount of the payment/receipt (shown in the payment/receipt details box near the top right of the window) and the analysis total (bottom right) both show 0.00.
If you then go into the same screen again after clicking "Save", you will see the remaining balance showing as outstanding on whichever was the greater - in my example above, that would be £1 still to be allocated on the payment.
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Vince M Hudd - Soft Rock Software
(I only came here looking for fellow apiarists...)