I had known my boss for a long time, even before working for him--my mom has worked there for a lot of years and is pretty chummy with the boss man--I guess my experience is a little different but I suppose I'll share anyway, maybe it'll give you some ideas, who knows!
Basically what I did was e-mail my boss and ask for a private meeting, where I calmly told him and his "second in command" about being trans and the sort of stuff they might expect happening to me in the near future, such as name change, doctor's visits (until I received my testosterone), etc. After that, we talked about who we were going to let in the know and how, as I work as an accountant at an auto body shop and it wasn't like I knew all the mechanics and body techs super well anyhow. In the accounting department, I let my boss tell my co-workers, since I really didn't want to be awkward and pull everyone aside to tell them, and I was a guy who very quickly cried in the face of confrontation if I felt overwhelmed. Our company is small, so we don't really have a whole department for HR, only a new employee that I didn't know/trust well enough to confide in first. However you manage to tell everyone at work, I'm sure it'll go over fine, judging from what you've mentioned of your situation, and I wish you the best of luck!