From experience, I can tell you that this is best done while small children and the yarn-prejudiced are not at home.
Have your empty bins handy, and load the yarn into the bins according to category. Create categories that make the most sense to you. For example, my categories are:
1. Sweater yarn (sweater quantities of worsted yarn)
2. Tee yarn (yarn for short-sleeved garments)
3. Sweaters made of itty bitty yarn (sport and fingering weight in sweater quantities)
5. Cottons and linens
7. Sock yarn
8. Super fancy-pants sock yarn
9. Acrylic and baby yarn
10. Single skeins (not of the cotton, lace, thread, sock, or acrylic variety)
The next step is to build a fort out of your bins.