Your question is kind of interesting to me as I present largely as an effeminate male right now, and have been transitioning since February of 2013 until now, and started HRT in early September. I came out to HR in September, and my peers and boss around the same time. Essentially, I have long hair, earrings, painted nails, and wear women's pants and shoes quite often. However, I never officially transitioned. I just told them I was transgender and this is how I express my gender. Right now nobody seems to bat an eye. You should keep in mind that I identify non-binary and my presentation waffles between butch female / femme male quite often.
That said, I made very clear that I plan to progress on HRT and may go full time and further change my presentation to more girly in the spring / summer of 2014, and that is what we are working with now. I think the big things I have encountered so far is a complete lack of knowledge on the part of management and HR. Through a local trans support group, I connected my HR representative to another HR rep at a company that had a member of my support group transition so they could share ideas. I had to identify all of the specific issues that we would need training on and targeted groups to train - I work in a 3,700 employee manufacturing company, and I am a client manager supporting production for detailed cost analysis. It's a very blue-collar male environment.
To that last point, so far I have not had too many challenges in my present appearance. My immediate work team and colleagues are professional and started asking questions when I went from clean cut male in khakis and button down shirts with sweater vests to skinny jeans, andro blouses, earrings and Sperry's. I had a serious meeting with my manager and HR and explained what was going on. I came out to my three closest work team members at a lunch informally. They have all been pretty nonchalant or actually supportive.
The only issue I have had so far, and I don't have an answer for, is there are some manufacturing managers who are real "meatheads" who clearly are uncomfortable with my presentation. They don't give me a hard time because we are pretty open with LGBT protection policies. However, my male privilege has gone out the window. By this I mean that a year ago I would go into a meeting and be an equal part of the discussion, and could interrupt someone talking if I disagreed with them and they would shut up and listen. I could also bust their balls if they had an opinion I did not agree with and they would back down or banter with me. Things changed when I got earrings, and especially after I went in with purple nails (I look very middle class, working professional, and not younger alternative - it is work appropriate female attire). In general, women seem more comfortable and accepting than males I work with.
The best I can say now is that I sometimes feel "tolerated" in discussions, and need to be pleasantly persistent lest I be perceived as antagonistic. It is tough for me to interrupt without getting unfriendly looks. Better is for me to feign interest, and then say something like, "Well, that is an interesting perspective. I wonder if we might consider doing this as an alternative." It is subtle changes to language and I see cis-women doing it. You will have to work twice as hard, have half as many personal issues, and do it all with a smile to be taken at the same level of competence as male counterparts. Really.
I think the biggest issue is going to be bathrooms, and I am pushing my company hard for a unisex, non-gender bathroom. Aside from that, I think the other item is to do as much homework before you meet with them. Have a plan and identify several issues, specific needs, and recommendations. I think the Human Rights Campaign has some brochures you can download to help employers with transition policies and training. You will probably get initial support - but you will want to assist them in understanding what it means and what they need to do. You also need to be honest with yourself and stick to commitments with them - if they are going to spend money on resources for training, changing bathrooms, etc. then you want to make sure you have your transition timeline worked out so that it does not lead to confusion.
Good luck!
