an easy way to store scraps is in a gallon ziplock baggie by colors.
there really isn't any one right way to store scraps. you need to first look at how you store full size paper... vertical in files? then perhaps the scraps can be in a baggie in the front of the file
horizontal? then the scraps in a baggie on top?
good luck finding what works for you!
its always an adventure. I think I tend to reorganize far more than I actually scrap!! lol