Steripens are designed for use in 1/2 liter and 1 liter water bottles; there are two settings. Using a Steripen in your 3 liter Camelbak will probably not purify the water nearly enough. Forget that idea.
I carry a 1 liter bottle and refill it as it gets used, then use the Steripen. There are usually water sources along nearly every Eastern Sierra trail, from which you can refill a bottle. I haven't used my Camelbak containers for the last 5 years.
If you get sick from Giardia (slight risk), don't worry, see your doctor; you'll get over it.
