What works for me at Jo Ann's is to give the cashier the coupon and item together so he/she knows which item gets the 60% and which one gets the 40%. You'd think the cash register would automatically take the 60% off the most expensive item, but it doesn't always work that way.
I haven't shopped at Jo Ann's in quite a while. My boss's wife is a fan of Hobby Lobby so he gives me Hobby Lobby gift cards for special occasions. Unfortunately, I haven't found a lot of fabric that I like at Hobby Lobby so I use the gift cards for batting, notions, etc. Not as much fun as shopping for fabric, but I'm not going to complain about a gift!