Kacey,
You may not have a choice as far as telling your boss. If you don't have all your credentials legalized, you will still need to have paychecks written in your current name or you won't be able to cash them. Also, your bank account, if under your current name will probably not cash your checks for direct deposit if the check has a different name on it.
There is really no need to out yourself to other employees, just the boss. Then, ask you boss to keep the fact that you are a transgender private and to back you under the name you choose. Sometimes things get out anyway, but I don't see a way around telling the boss if you want to get paid.
Sam1234