Just write them like any other character. Just because their gender isn't what they feel it should be doesn't make them anything different. For the most part, transgender people act like the gender they feel they are.

Trans people experience adolescence and puberty in different ways than non-trans people do. I'm wanting to write a story with a socially awkward nerd who happens to be a trans man. His transness won't be the most important thing about him but it will be an aspect.