Thanks to Suzanne for this Frugal Baby Tip!
I'd make them no more than maybe 5 thick layers of flannel -- make one and use it to see if it dries in the same amount of time as your other diapers. Stuff that is too thick breeds bacteria because it never gets fully dry.
I'd just measure the size you want the final stuffer to be (maybe you have a favorite one you can trace) and cut out 5 and stack and sew around the edges with first a straight stitch and then zigzag (or something more fancy, if your machine has more stitches).
If you're just making rectangles you can just cut a long rectangle and fold it up from the short size to make it several layers thick.
Happy sewing.... I love my green towel and denim contours!