thats seems unreasonably controlling. Are you sure she isn't suggesting using these as I cannot imagine anyone telling you which software to use.
By the way, I use Endnote and outlook. Both are very good, you just need to get used to them. I tested procite before i used endnote, and endnote is the easiest to use.
Just be firm, and say, 'actually I would prefer to use .....' and if she says otherwise, ignore her and do what you want. Can't see that standing up well if she complains at your other supervisor 'boo hoo, she won't use endnote like i told her too!!', your other supervisor will then think she's being petty.
Keep a log of everything she asks you (or tells you) to do, so that if your other supervisor says that you haven't been taking advice on board, you can reel off the list of things that have been asked of you, and why you chose not to do it. That will soon shut her up if you reason why you don't take certain instructions.