You need at least 18"-21" above the door for a standard headroom door but they usually will tell you 24" to be safe. You can get low headroom doors that look and function just like a standard door but they are more expensive.
My first real job was installing garage doors and fireplaces.
You can get away with 12" of headroom and that will allow enough for a door opener above the door.
They do make low-headroom track kits where the top roller of the top panel rides in a separate track, but if you're building new, avoid this - they don't work as well as conventional. On extreme applications, you can get into rear-torsion low-headroom (where the spring(s)) are mounted all the way at the back of the horizontal track.
You can stay with a residential door - they usually are made in 18"-21"-24" panels, and you CAN mix them to achieve the desired height of the opening.
Cosmetically, If you do it right, it looks fine.
It's then a simple calculation of the weight and height of the door to properly spring it.
Todd, If I can be any help PM me, I'll send you my #.