Hi Susan
All three of your options work.
My first choice is to do it as a negative check in an AR cash batch - not only is there a certain logic to it, but it is by far the easiest method if you are reducing the balance of multiple transactions.
Doing it as a credit note is my second choice, because it doesn't require thinking about debits and credits, like entering adjustments does, especially if we are talking about a single invoice balance needing to be reduced. But you would be forced to do it as an adjustment if some of the transactions are themselves credit notes, adjustments or unapplied cash.
Steve