If you are doing pot holder size, you could place a piece of newspaper print or low weight copy paper under the batting. Remove the paper when finished. Use a seam ripper to snip the paper in between the sewn seams. Fold back the paper along the seam and it should snap off.
You could also use the very very thin cotton fabrics sold in some local retailers and place on the other side of the batting. Then sew the 2 sides together. I have seen this thin fabric at $2.00 a yard locally, so if concerned about the lint from the batting, the cost is minimal vs. cleaning the machine constantly. That thin layer of fabric is not going to make a difference in the middle of the potholders.