If you really trust him, there's no reason to be nervous. Sex isn't as big of a deal as people make it out to be, you're not taking 10 hits of acid, it's not going to do anything scary.
If you're nervous because of DYSPHORIA, which I'm guessing might be the problem since this is in the trans forum, just make sure he knows what makes you uncomfortable. My partner and I have physically heterosexual sex without me ever feeling uncomfortable because he -never- treats me like a "girl". He doesn't play with my breasts or nipples, if he talks dirty he never refers to any of my parts as pussy/boobs/tits/cunt/ whatever, he doesn't make a big deal out of my hips, he never really does anything that he wouldn't do to a physically male partner. If your downstairs bothers you, make sure he knows whats ok and not ok to do, some transfolk love their partner touching them, some only do penetration but no touching, some won't have vaginal intercourse, just let him know what you're comfortable with. By top, do you mean penetrate him with a strap on, or just be on top of him?