I would suggest not bothering with a car. Boston is a very difficult city to drive in these days--you never know what streets are going to change or close due to construction (although it shouldn't be as bad in October as it is now, as most of the Big Dig stuff should be done by then). It's really much easier to use public transportation, cabs, or your own two feet. Boston is a great city to walk around--I think you soak up a lot more of a city's atmosphere when you walk it than when you take a car.
You should look into taking a Duck Tour while you are here. It's a 90 minute tour of the city by land and by water. It's a lot of fun. The Ducks leave from the Prudential Center, and the Museum of Science.
One of my favorite restaurants is Fire & Ice on the corner of Berkley St. & St. James. It's a Mongolian grill--basically you pick out the meats, veggies, pasta, and sauce you want, and bring it up to the grill for cooking. It's a great deal at lunch time Monday through Saturday--just $7.95 all you can eat. It's still a good deal at dinner time at $17.95.
The Boston Park Rangers (or something like that--can someone help on that?) offer walking tours of historic sites in the Downtown/Fanuiel Hall area. They have on Devonshire Street near the State Street T Station.
There is a Farmer's Market near Fanuiel Hall every Friday and Saturday. It's really packed, and there are tons of vendors.
If you are up for a good walk, you should consider walking the Freedom Trail. Just follow the red line on the sidewalk to many different historical sites. A good place to start the Freedom Trail is at the Boston Common, where there is a visitors center.
Oh, and just as an aside, I walked up Charles Street today for the first time in a while, and it wasn't as much of a hill as I remembered (it's more at the bottom of the hill). I saw where the Charles Street Inn is, and it's pretty much in the middle of Charles Street. It's not a bad walk to the T.
Karen