Azureus and uTorrent are clients of the Bittorrent protocol which you already have included, so no worries, your setup is fine. Just make sure you apply it on the correct WAN interface on the outgoing flow.
I have it applied to the outgoing and incoming connections for the bridge. I beleive that is what the guide has instructed to do.
We have a quad core box, 2.4GHz with 4 gigs of ram and gig ethernet connections. What type of bandwidth should we expect to be able to push through this box? WE have a 60meg up and down fiber connection, with roughly 320 users (no idea how many concurrent) that will be behind this box. Will this set up handle this? I have read where it should do just fine, just seeing what you thought.