The batting can certainly be folded as long as you are still able to quilt it. IF you are quilting my machine, will it fit under presser foot? IF you are quilting by hand, try a practice sandwich first. I use cotton batt and thing it would be hard to quilt a double layer. Poly is light enough but, if it is a high loft poly, I think yoiu would have to use a large utility stitch. You aren't going to be able to load needle very much.
For durability, the double layer is not necessary, just be sure to have a good amount of quliting.