This is the way I remember (vaguely) of making puff quilts.
1. Cut the base size of your choice, say 4 1/2", out of muslin.
2. Cut the top piece larger, you would just have to try this part because I don't remember the size.
It needed to be enough larger than the base to be able to make a pleat or fold in the fabric, on all four sides.
I would say somewhere close to an inch larger than the muslin, to allow for the pleat. Just pin at the 4 corners, and pleat what is left between the pins.
Leave a small area of seam open so you can stuff a piece of poly batt between the muslin and the top.
You could do the stuffing with the needle down, and then just finish sewing the seam.
I would probably start my seam just shy of the corner, sew around, leaving the corner open to stuff, and then finish sewing around the corner.
3. You sew these together strip fashion, and then sew the strips together.
You don't use a whole lot of stuffing, just enough to make it pop up in the center.
Joyce