I've been canoeing in the bwca and the Q for many, many years, two trips every summer.  At first I hung the food pack over a tree limb but a) you can get hurt trying to throw a line over a high branch becaus you need to attach a weight to the end of the line and that weight usually ends up being a rock that often comes very close to hitting you on the head at some point, and b) the frustration and effort of finding a place to hang the pack and getting the line over the branch, etc., wastes a lot of time and energy and puts me in a bad mood.
I have stashed the food pack in the woods like Clif Jacobson recommends and I've never had any problems.

Also, I never filter my water and I've never gotten sick.  I learned a guy working for one of the Ely outfitters who told me that he wasn't supposed to say anything about it, but none of the people working for the outfitter filtered thier water.