Trouble with Payments on Vendor Account

My company has recently moved to NS and we are having a few issues with payments on account. We have a number of suppliers that will only deal with us on pro-forma. We make payment of the proforma and are struggling with dealing with the payment that has been made. I know that we should really be posting htis as a vendor pre-payment, but the issue is that we have such a large volume of invoices that once the “tax invoice” is received it gets processed and as the pre-payment does not show up on the pay run reports we end up paying the same invoice twice. In our old system we could simply post the payment as a supplier payment on the vendor account, but this does not seem to be feasible in NS.

Is there a way of posting payments onto the vendor account so it is taken into account when pulling a full pay run? I know that vendore prepayments can be auto allocated against an invocie, but this is also not working in our case as a number of invoices do not have PO’s.

I never thought Sage would have been better than NS, but it appears to be the case unless I am missing something really obvious.

Thanks in advance for any help!