Hola from Boston
1. Not all Subway station have the "new payment system". Actually most of them still use tokens so do not buy a card with much credit.
2. It is very easy to get to Seaport and to HI-Boston with the T. Both are less than 2 minutes from Subway stations.
3. Freedom trail is a must. It takes 3-4 hours if you stop for photos (& ice-cream). You can do it yourself. A map with info is available for $2 at the info center (Park station).
4. Nightlife - the area near the Fenway park (home of Red-Sox) is the spot, with lot's of bars and night clubs. Avalon is a nice club. Yesterday the cover was $15. Drinks are quite expensive ($10 for vodka-redbull).
5. HI-Boston is a very nice hostel ith nice people but the rooms are very small.
6. Seaport is great :)