You are talking about the quilting? You may need to adjust the tension on the machine because of the thickness of the quilt. It's always a good idea to make a little test sandwich and practice on that until you get the tension right. In this case, if there are loops of top thread on the back, it sounds as if the top tension needs to be tightened (turned to a higher number). You need to adjust the tension until the back looks just the same as the top.
Were you free motion quilting? Stitching in the ditch? Using a walking foot?