I have been flying as a passenger on Cape Air for as long as I can remember, really an excellent operation. Some of the nicest people to deal with, especially when KBOS has bad weather and/or the KACK tower is opening/closing every few minutes as fog rolls in/lifts off the south east corner of the island. One evening we were on approach to KACK when fog closed the tower, pilot circled a bit to see if it would push off, eventually diverted to Hyannis. Not even 5 min after touchdown in Hyannis the KACK tower reopened, before anyone even got off the plane our pilot asked if we wanted to taxi back and try again, 15 min later we touched down at KACK.
As far as sitting in the right seat: a gate agent/ramp agent will escort the passenger group from the gate downstairs to the ramp, I believe the same person usually assigns seats once you get to the plane.. Sometimes they board in whatever configuration the group arrives at the plane, and sometimes (presumably when weight and balance is at issue) they pick a few people and tell them where to sit, then the rest go wherever.
It can't hurt to ask the person who escorts you down to the plane about sitting up front, I have heard many people request the right seat, I can't imagine them saying no unless they have a FO is on board or the flight is carrying a lot of cargo or something? Good luck and enjoy the flight!