I use Coats & Clark Dual Duty or XP for most piecing on the top. It's supposedly 50 weight but seems thinner than the 50 weight machine quilting thread. I use prewound bobbins 2 ply 60 weight, for piecing and most quilting. I will occasionally use the same 50 or 35 weight quilting thread in the bobbin if I want the threads to match or if I'm having trouble getting the tension adjusted.
Robison Anton makes a very nice 50 weight cotton that just flows through my machine and costs much less than King Tut which is also very nice but I have to use a larger needle for it as it seems thicker than 50 weight. The Robison Anton is harder to find and has fewer color choices, though :(