The Joanns here will take a 50% coupon off of sale items; they override the sale, then take the 50% off of the original price.
Most stores that are offering BOGO (buy one, get one free)give the lower priced item free. If you are getting three items, good idea to have the cheapest one rung up separately.
The only fabrics I buy at Joann's are fleece and Kona muslin; I've never had any problem using a coupon off of either - but have never purchased over 10 yards at any one time, so don't know if that would be a deal-stopper or not.