My boss won;t get out of my way

Many organizational changes took place in my department earlier this year. My boss was promoted, I slide into the role and an additional layer of management was added as my direct reports. A couple of really bad management choices made in order to work around people's feelings and not what's best for the department. My boss is over multiple departments and will not physically / emotionally move out of the department. Constant conversations of reporting structure yet she jumps over me to the staff and allows them to work around. Ultimately, there is a lot of confusion as to who to go to for what and when. Also, her song changes depending on day. I have asked he r to please move out and she will not. I need her to leave so that I can lead the team and not just be the bad guy instilling accountability and knocking out a ton of projects. Help!