I cut mine in rectangles that are bigger than my inserts so I can wrap them around the edges a little. It protects the insert from poop and gives a little wiggle room with shrinkage. Mine kept shrinking even after I prewashed them, so this helped a lot.
This might be something everyone but me knew, but I would recommend not drying the fleece liners in the dryer, at least not with diapers. My prefolds had yellow fuzz all over them the first time I did this! Now I just hang the fleece with my covers and no more shedding.