Instead of adding something to refund them, cancel the subscription and then immediately generate a bill run for just that account. it will create a negative invoice that you can then apply to the open invoice created by the refund.
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It would be nice to be able to specifically select a due date for invoices. We are a due upon receipt company however we charge monthly rent that we bill ahead of time due on the first. Our invoice date is then the first so our due date can be the first instead of the invoice date being today and the due date being the first. We went the rest of our invoices to be due upon receipt however.
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