1) The chair should stay in the room. The idea is to let ARC "see" the room just the way you will be using it, as much as possible.
2) When I set up my room, I would crouch down behind the chair while the test tones were being generated, trying to make my body's aural fingerprint in the room as small and inconsequential as possible. Other people may have other ideas about that.
Good luck getting things set up. If you take your time and do it very precisely and correctly, you won't be disappointed. I know that I am very happy with the results I got.