Yes, or have your TA call. The thing is Special Reservations are the only people who can block an accessible room and have the confirmation indicate it is a "guaranteed" room assignment. The regular reservations people cannot do this, they can only put that one is "requested" which in your situation is probably not acceptable.
Though I do not use a pc, some of the suggestions that I have seen from people who do use the follow:
1. Have your technician mark (with bright contrasting paint) the tie-down locations. This may be necessary for the aircraft but an absolute necessity if you ride the buses.
2. Bring some heavy (duct) tape to keep loose parts (such as footrests) from being moved at all when the pc is stored on the plane.
3. Be sure to remove the control box/joystick when you go to board the plane. See if you can get a padded box to keep it in.
4. Attach a sign, preferably with pictures, on how to put the chair in freewhhel or lock.
5. Note that any medical equipment or supplies you bring aboard the plane with you do not count against your carry on limitation. Since you will be the first to board you will have sufficient storage room for anything. Note also that you will probably also be the last off the plane.