Are you using Reynolds freezer paper? I have never had a problem sticking the waxy side of it to fabric.
When I did this, I ironed the freezer paper onto the back of the yardage before cutting squares. Much easier than cutting squares first.
Instead of just drawing lines 1/4" from the edge (to keep people from extending their signatures into the seamline), I would experiment with adding blue painter's tape along the edges -- maybe the inch-wide version. This would likely keep extravagant signatures within the lines!