When I managed an ops area for a credit union, our process for placing a stop payment on a check evolved to include placing the same stop payment on the ACH side. They only signed the check stop payment form and paid the one fee - since technically you're only stopping the check transaction.
Our core processing system had a field for "check number" for the ACH side as well. Which meant that if you placed a stop payment for check # 2101 for the amount of $211.90, the stop would be effective on both the ACH and check processing side.
We did not notify the customer of the ACH stop hold or anything like that. We pretty much just took the stop payment order from the customer and ensured that the check would not be paid, whichever channel it came in through. I don't believe there is any requirement to tell the customer that his check might be presented via multiple channels.
_________________________
CRCM + CAMS = certified compliance nerd
Opinions expressed in these threads are my own and not my employer's.