The same thing you do in any other relationship - you talk about it!
I suggest that you schedule a meeting with her, preferably early in the morning (not at the end of the day when she's probably more stressed), and tell her as openly as possible what bothers you. She may not be aware of some of the things she does, or how she makes you feel. Try to be very constructive in your criticism - tell the good and the bad. If there are things about her that you appreciate, tell her about it. Try to be balanced. Speak about how she makes you feel, not about facts. It's impossible to argue with one's feelings - they're subjective. If something makes you feel in a certain way, then it must be true. Why it happens, whether it's justified or not, and how to respond to it can be argued with, but not the fact that you feel what you feel. I hope I make myself clear.
Finally, come to this conversation with an open mind. Be prepared to receive criticism and learn from it. When she tells you something about you, don't rush in and try to respond or explain why she's wrong. Just listen quietly until she finishes, and repsond after that.
I hope this helps. Good luck! 