Yes, you either need to get the toll pass or pay the excess fee (which can be quite pricey depending upon which company) when they eventually bill you for it.
If you are staying in Back Bay, I would HIGHLY recommend not renting a car the whole time - parking around there is a pain in the neck and very, very pricey. If you absolutely need a car, rent it from a local place around the hotel, and only for the days you absolutely need it. The best route depends on where you are going. Easiest would be the pike out to 128 (er, 95) and then north on 95.