Frankly, I seem to have more success when I use the invisible thread in both the top and bottom. When I use cotton in the bottom, I have more trouble getting the tension right. I also think that the brand of thread you use has an effect. You probably have to experiment with your particular machine. I found that different brands act differently in my machine, no matter what the settings. Once you find the one that works best, however, it's a pleasure to do the quilting. By the way, the Harriet Hargrave books have some fantastic suggestions on using invisible thread, such as using extra thread guides to help take the "spring" out of the thread as it feed through the machine. Your library may have her books, so you might check it out there. I've learned a ton from her!