I quilt on a Bernina and have never used two layers of batting. Yes, check that you are using a new sharp needle maybe 14 to 16 size. You are going thru two layer for cotton batting probably with two layers of scrim. That is a bit of bulk in my opinion but I have read threads where it has been done. Not sure if it has only been done on a long arm. Be sure your quilt is supported as PaperPrincess mentioned. Hang in there.