Supplier Ledgers and Transactions

I'm thinking of moving to some accounts software but I have a general question that I was wondering if anyone who had used similar software before could answer for me. In software such as Sage and QuickBooks, etc, do you tally a transaction to a supplier's ledger, or do you tally a transaction to a supplier's invoice. The problem I've got is we sometimes pay off general amounts of credit accounts, for instance

Invoice 1 5000 Invoice 2 7000 Invoice 3 8000

We might then pay 6000 which obviously covers invoice 1 but only part of invoice 2.

Basically what I'm saying is, we sometimes pay multiple invoices with one cheque, and sometimes multiple cheques for one invoice !

How do software accounts package work this? Do you just have a general ledger with transactions and invoices, and no way to actually tally payment(s) to an invoice(s) ?

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Einstein
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