Heavily starching flannel before cutting really helps. I mix up a 1:1 solution of Sta-Flo liquid laundry starch and water, "paint" this on the fabric using a large wall painting brush (until the fabric is saturated), toss in the dryer, then iron with steam. The flannel comes out with the stiffness of lightweight cardstock and is *not* going to wiggle around or distort on you while cutting and piecing. It makes piecing flannel a lot easier, and also helps prevent puckers when machine quilting (heavily starch the backing fabric also). After the quilt is bound, wash in the washing machine to remove the starch.
Edit: Oops! Sorry, I just noticed the comment about a ton of 2.5" squares. If they were prewashed, then you might be able to use a similar technique to the above but lay them flat on toweling to dry before ironing. If they haven't been prewashed, then starching them may result in serious shrinkage and distortion of the squares -- in which case you would be better off just using them as is, or possibly you could experiment with spray starching a few. (Spray starching is a much slower process than the yardage technique above.)