Here is what I have learned. Cotton will hold up better than polyester. Use the same kind of thread on like fabrics, cotton fabric and cotton thread. Polyester is said to cut thru the cotton fabric and it won't hold up as well in the long run. I don't know if this is true because I haven't tested it. Same thread in top for sewing as in the bobbin; lots less headaches when they match. I try to use mainly cotton thread when quilting and when piecing, I always use Aurifil. It is a 50wt 2ply thread. Its very strong and low lint. I started using it for piecing because I couldn't get my blocks to come out to the right size; the smaller the block with more seams the more off it would be. Having only 2 ply makes a big difference and now my blocks come out good. It's a good thread with lots of colors even though I normally use a natural color and then it blends in really good.
I'm not knocking polyester and use it when I'm embroidering or other things.