I <3 JoAnns because of their coupon policy. You can use mulitple coupons in one transaction as long as they are different coupons, so you should be fine. They also accept Michaels, Hobby Lobby and A.C. Moore coupons. They could be paper or off of a smart phone. I just usually pull up my GeoQpons app and use the coupons right from there.
Joann's policy on this is generally one coupon per transaction, most (aka every single one that I've been to) will scan as many as you give them. So technically you probably can't do it, their computer doesn't prevent it, and most of their employees won't stop you.