I think the best way to approach this is in a really professional way. Arrange to have a meeting with her and tell her its about the current situation and issues you want to highlight. Then at this meeting just tell her how you feel for example, "I feel that we are spending to long discussing endnote/referencing rather than getting to the point of my actual research and this worries me because I want to finish my PhD is less than 10years".
Ok, the finishing in less than 10 years is optional but I think you get the idea. If you put everything across really professionally, she can't object or bitch at you.
If this still doesn't work, you really need to talk to your main supervisor.