The best thing you can really do is to tell your boss one on one what the deal is. She would be able to tell your coworkers your preferred name and pronouns for you if you like, and ask them to not question you about it. Also, it's easier then you think to work out something with the bathrooms if there isn't a male or gender neutral bathroom available (like come in a few minutes early to change and do your business, or whatever else). Coming out is obviously not easy, but in some cases I think it's necessary.
For all my job interviews, the first thing I want to be sure of is whether or not being myself being trans is going to be an issue, covering my name(name tag), pronouns, and bathrooms, and so far it hasn't been one as far as I know. That is to say, I live in a state where it's illegal to discriminate because of gender identity, it's still something that needs to be talked about so I can be sure my boss and co workers can be as comfortable as I am while in our work environment.
I don't know where you live, so I'm not entirely sure on how stable your job would be if/when you decided to come out, so I would suggest finding that out first before anything. If it's okay, I think what you should do is tell your boss you need to talk and express your concerns directly, because it's the only way you'll be able to get things done in this situation. If not, I would suggest waiting awhile and try to get to know your boss better and to find out if she's okay with that trans community. I would have high hopes because she's gay, and most gay people from my experience are okay with transgender folk, but there are also people part of the LGB side of things that don't accept transpeople, so I suppose keep that in mind.
Regardless, what's important is your comfort while you work; we all have that right. But if it isn't possible at this place, the only thing I could suggest is either quit unless you're in dire need of cash, or keep working there as if nothing is going on.
I hope this helps you out at least a little bit and I wish you luck.
-RJ