I quilt with Sulky invisible nylon and use regular sewing thread in the bobbin all the time. Takes a while to get the tension just right, but I really don't care for the look of most colored threads....I feel like they compete with the blocks and sometimes make the quilt look just too busy. I find that FMQ with invisible thread looks the most like hand quilting.

I used it for the first time last week, in the bobbin. I was FMQ, so didn't want the bottom thread to show on the top. Worked fine.