The Brick Manager app might be helpful with sorting the sets. It keeps track of all pieces that you've found and which are still missing.
Note: I am the developer of the app, and my post is a genuine attempt to help the topic starter and others facing the same issues.
Here's a description of the app from the app page on the Play store:
You have a huge ...
I bought a desk organizer insert with 9 bins in it. I put parts with the same color in one of the bins. If there's a lot of one color, I split it into another bin by size or type. If you're building a set, you can do this bag by bag as you work through the instructions.