I agree with the suggestion to use a scope foot (or whatever your brand of long arm takes to help ride over the thick parts of the applique and I also would recommend trying a polyester thread. I use Superior's So Fine 50 weight which is about the same thickness of Aurifil 50 but is stronger. I tried Aurfil on my machine once when I first got it and had trouble with thread breakage. I was new. I maybe would have better success with it now but I love the way So Fine looks. It has a matte finish compared with Glide thread and it fine enough that I don't often notice the thread itself after quilting. Oh, I think you could also try bottom line in the top, I know some folks have done that.