I first used the Jo Anns clear ... nothing but trouble. I use Superior or from Clotilde. Much better results. It is best to use regular thread in the bobbin, but I have gotten brave and used it for top and bottom a few times. It just a pain to wind a bobbin and keep it from stretching the clear thread.
If you are quilting a darker color ... use the smoke colored it does not reflect as much light and is more invisable on the dark fabric.