Hi Travis
Welcome to Poker Strategy Forums. I hope you like the site. We have some great members here who are very friendly and helpful.
As far as recommendations for other sites besides PokerStars, you can check check out the
Poker Sites for US Players thread the sites are listed basically in order of volume. Like Powda mentioned
Full Tilt is a great site but you may also want to check out a site like Cake Poker or Bodog also. The low limit action at Bodog is especially weak.
As for your second question about tracking software.
Poker Tracker is probably the most widely used and has a new version out, but I actually prefer
Poker Office, it's a little easier to run out of the box and works well. The feature I like/use the most is the automatic showdown of the opponents cards (on most sites), so you don't have to go back and constantly look at the hand history, just to see what they had.
Once again, welcome to PSF
Jason