how do I post a cheque for a prepayment to a supplier when there are other outstanding invoices for this supplier without the program applying the cheque to an outstanding invoice
You could create a “pro-forma” Supplier Invoice and allocate the payment to it and when the actual invoice arrives adjust the “pro forma”, or
Post the payment to an Asset Prepayment or Clearing acct and reallocate via Journal once the Invoice arrives.
You also have to consider whether you care. The supplier’s total balance in
Accounts payable will be accurate. When you receive a formal sales invoice from the supplier and enter it as a purchase invoice, you could reallocate the payment you made as a deposit to it. Or, if the payment has been automatically allocated to an already existing purchase invoice and you later make a payment that you also allocate to that previous invoice, Manager will “bump” the undesignated deposit to the oldest remaining purchase invoice, which by that time may be the one you want it to be. At the bottom line, monies paid to suppliers are fungible in most cases.
Only if there is some specific contractual reason why things need to be kept separate do you have to use one of the techniques @Brucanna suggested.
Good housekeeping provides more accurate traceability, rather then bumbling mismatches between invoices and payments
You can date the invoice to a future date if needed so that the invoice expense falls in the correct accounting period whilst the payment falls in the current period. Its not ideal as you may mismatch dates but could be a simple way to then allocate a payment against a specific invoice. It saves on creating journals and keeps everything in one place.
Alternatively, if the supplier does distinctly different services then you may decide to keep all invoices that relate to a particular service as a separate supplier. Payments can then be allocated relating to one particular type of service and may help when there are lots of different invoices.