I photocopied each page and inserted into the clear sheet protectors and stuck them all in a 3 ring binder. This allows me to pop out sheets if a player needs them, the book is listed on each sheet so another can use the Companion to reference the item too and it saves wear and tear on the books.
I have a binder with everything needed for PC Creation. One got GM-ing with weapon tables, crit tables, charts, MM tables, Random encounters, etc. One binder with GM/PC goodies like treasures, poisons, herbs, etc.
It made a huge difference as a GM when it came to character creation and gaming. Given the number of skills from all of the Companions, you'll never get them on 1 page with descriptions (and the companion from which it appears), lest you have magnifying glasses.