My very favorite quilting website with my very favorite method of organizing scraps:
http://quiltville.com/scrapusersystem.shtml
Hope you like it!
Take a look at some of the quilts. It's definitely worth the cutting and you will lose next to nothing in terms of waste fabric.
If you end up with any shreds and confetti use it to stuff pet beds or toys that are best with pure cotton.
Have fun and happy quilting!