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I've been having the same problem. This is how I get it to take the transaction.
On the invoice line, make the payment, the amount of the invoice, not the amount of the payment. Then click "resolve difference", then add the resolving transaction. If they payment amount is not the amount of the invoice (next to the invoice), then it wont take it, it will just complain it cant resolve the difference.
See, my customer had made a payment of 124.53 and quickbooks will put that in the PAYMENT field, but you just have to change it to 147.88 and then resolve the difference. I don't know why they made it confusing like that, but this method works.