All of my 8 1/2" x 11" cardstock is stored using a wire paper rack. I purchased this rack years ago from a craft store that was closing. But no matter what method you use to store your cardstock, my system can help you stay organized.
I store my cardstock by Stampin' Up! Color Families... Brights, Subtles, Regals and Neutrals. I find this method helpful since some colors are very similar and sometimes tough to figure out... is it Blushing Bride or Petal Pink or is it Pool Party or Balmy Blue? So I keep the cardstock in the order of the color chart I printed from Stampin' Up! I keep the color chart on top of the paper rack for easy reference.
I keep my White Cardstock and my Thick White Cardstock at the top of the rack since I use them so much. I also keep the current in-colors at the top of the rack since they rotate every two years.
I think it's important to keep my paper scraps and use them. I would forget about the scraps if I threw them in a drawer. I purchased clear folders from Staples and I keep the individual scraps in the clear folder on top of the coordinating cardstock.