Personally, if you are "new" to Amtrak travel, I'd opt for the Acela. YES, it cost quite a bit more than Amtrak's other option, the Regionals. BUT, since you are making this a trip, and not a daily commute, ENJOY yourself. Make sure that you also register and sign up for Amtrak's loyalty club, called
AMTRAK GUEST REWARDS.
It's a pretty good way to earn free rail travel, and not nearly as hard to earn rewards as most of the Airline loyalty clubs.
Current AGR members can also get a referral "finders fee" (in points), if you join AGR, and then travel within 90 days or so. (but they have to send you a LINK)
As other posters (OP) stated, sit on the right hand side going north. You can get off at either Back Bay or South station in Boston. I prefer South, just cause I think the food and amenities are better. You can catch the subway to North station from either Back Bay or South though.
If you are so inclined, you can bring your own snacks and non-alcoholic bevs on Amtrak. (if you ever take a long distance (LD) trip in the future, and reserve space in a sleeper (roomette, bedroom, or family bedroom) you can even bring along your own choice of "adult beverages" for personal consumption.
But on your ride up the east coast, bring a book, your iPod/iPhone/MP3 player, and be ready to relax. Grab a window seat on the right. No need to actually PRINT your ticket, until you get to the station, that way there is no penalty if you need to change it.
Virtually all Regional seats, all Acela seats, and the DownEaster seats should have AC outlets, should you need to charge anything up.
Lastly, (sorry to rant) Book AS FAR IN ADVANCE as you can. The further ahead you book, typically the lower the rates will be. If you are a student, AAA, student, or Military, you an also get a 10% discount on your rail fare. (but not on the Acela trains, no discounts at all there)
Right now, looking several months out, the one way (OW) Regional fare is (SPECIAL) is $68, the Acela Business Class is $152, and if you REALLY want to go FIRST CLASS, (which would include two pretty good meals, and any adult bevs, served at your seat) you could add another $114 to the $152 on the Acela.)
Go. Travel. Enjoy. Become a member of this looney group.