Take a look at this article on how to make custom door leafs - as mentioned by Steven. It is the only reasonable solution for your needs if you need more glazing than one row, etc, as provided by the standard garage doors.
It's a pretty painless process:
http://helpcenter.graphisoft.com/guides ... ain_walls/
You can model the door leaf/slab with any tools - typically slab tool with holes cut, but Morph works too. Thinner slab for the glazing, centered in the leaf slab. If you will generate drawings/renderings detailed enough to see it - profiled frames can be with the wall, beam or morph tools. Etc.
Try just a silly slab, the width/height of your door, and 2" or whatever thickness you want. Put some holes in it, save it as shown, and pull it into the garage door lib part as shown. That'll let you see how easy it actually is before you spend time making your real door leaf.