I use perle cotton--the largest size available. It works great. I try to tie them so the ends are on the back, not on the front to spoil the quilt top itself. I guess that is why I have learned to bartack on the machine. It acts the same way by holding the layers together, but doesn't detract from the finished product. Use monofilament on the top and thread to match the backing.
Anita in Northfield, MN