I have made many quilts with mixed fabrics with great results. I first wash them all in HOT water, then dry in the drier on it's hottest setting. Any shrinkage or other problems will have worked themselves out after that. I have used cotton, wool, and fleece all in the same quilt top and it has held up through multiple washings for over 10 years.
You will find if you are going to hand quilt, that the thicker, slightly waxy thread is much easier to work with than regular sewing thread.