Have used Poly cottons in the past, no probs except maybe the odd hand quilting prob when I have used something that doesn't hand quilt well. My main priority is always colour and so if I get some thing thats polycotton but works, what the heck.
Have even used Rayons in quilts, is terrible stuff to sew, but such fabulous rich colours that it can be worth the extra effort. Give everything a good wash before you start cutting. Another advantage that some of these manmade fibres have is that they often hold their colour alot better over time than pure cotton.