If the airplane does not require a SIC, then he cant log it as such. In 135 ops, that could change things, but you are pt91 so he shouldnt do that.
But that isnt your problem or consearn. The bosses are paying you to keep them safe. That is your obligation, and you need to address these issues now, not later. Not to mention, if he is busting altitudes and other regs, its your butt not his. You are PIC, you are the one who is going to get repremanded.
If it were me, I would approach the boss, sit down with him, and have a very calculating conversation with him. I would tell him that you understand that they are friends but you need to discuss these issues. I would tell him that you feel that it is very important that he is informed on the situation, and that the both of you, together, make a plan of attack to deal with the problem. He probably will want to know why you have waited to discuss this with him. I would tell him you havent yet had a talk with "wonder pilot" because you wanted to document these issues first, and then talk to him (the boss) about how to approach and handle this situation, again, out of respect for thier friendship.
On a side note, I wouldnt let him touch the controls until he can get you from point A to point B without getting you violated, and I would put strict weather/flight condition minimums on him.
Good luck with that