I am in the same predicament, but I was cutting the same number of squares from all three layers because I know how bored I get. I fmq 52 blocks and I still have to cut and quilt 48 - ughhh! You can put the top together with the raw eddges exposed and than sandwich it like a regular quilt but you will not have as rich rag effect since only the raw edges of the top will be showing. Another question is what are you going to do with all the batting squares that you have already cut?