Ok, this is probably the most tedious part of all scrapbook paper organizing—maybe even of all scrapbook organizing, period.
It's so important that you take the time to organize your paper storage
in a way that works for you. Sets of craft paper are extremely important since you'd be using them almost all of the time.
Thus, you'd want to properly organize them for easy access anytime you need them.
One of the most common ways is to keep your solid cardstock separate. Then gradually store them by color, and finally, sort your patterned paper by category or subject. You can also try to arrange them by size; putting all your 12 x 12 paper in one pile, for example, is a great way to stay keep everything clean.
For patterned paper storage (that doesn't have a set subject), you can divide them into groups like "paisleys" and "abstract backgrounds" so you still have a general idea of what you have. It's time-consuming, but you'll thank yourself later!