Wow, I hate to disagree with Plindsey, but as someone who has used NFL.com previously and purchased stat-tracker this year, I definitely think it was worth it.
If you have a pretty easy scoring system, then NFL.com probably works for you. But for me, having IDPs and several various scoring bits thrown in there, its just a lot easier to have Yahoo track it and update it automatically.
Besides, I have noticed discrepancies all the time between NFL's stats and Yahoo. At least last year I did. This year, I'm just going by Yahoo, since that is what my scores are based on anyways.
As far as multiple teams go, you will log into Yahoo, and after you launch Stat-Tracker, there is a drop-down box and you just pick the league you want to check out. It also tracks the other matchups for you in real-time as well.