I think the best way to go with this is to find yourself some patterns you would like to make and cut according to that. No use cutting 2.5 squares if what you want is 2 inch strips when you finally get to sewing.
The thing with Bonnie's system is it is a Scrap User's system not a Scrap Saver's system and that is how I use it. When starting a new scrap quilt I always start with my precut scraps and go from there. Sometime I don't even get to my FQs.