If you are using a longarm, I'm thinking for stitching ease it might be safer to use a cotton backing. The only reason I can think of for using a poly/cotton is for fading over time. Poly colors do not fade with washing and exposure to light; cotton colors do. Mixing the two types of fabric would be more problematic for the top, though; I can't see it mattering a lot if the top remains bright and the backing fades gently over time.
What kind of batting are you thinking of using? Polyester batting won't shrink. Once quilted, it is the batting (not, say, an unwashed cotton backing) that controls shrinkage.