My boss is getting on my nerves and I don't know what to do?

I share the office with my boss (unfortunately!) and he gets on my nerves. I like to have the office door left open and he likes it closed (this is all non-verbal language) I feel 'safer' when it's open. I haven't told him this though, as I feel intimidated by him at times. Also, when he dictates, he sits on the floor in the corner of the office behind me and I feel uncomfortable and it gets on my nerves . I just don't know what to do or what my rights are. I don't know if I'm entitled to say it makes me uncomfortable, as he's the boss!