Mark out the glass panel, plus whatever lining or framing being used and cut out, allowing double rafters width, along the rafter's you have just cut, similar to setting a stair well.
You may need expansion joints on some systems.
You should be aware that all glass supply and fixing are covered by a official body that I cant remember.
Google it, perhaps "glass and glazing safety"
If you see you're glass supplier with a sketch plan of you're needs then see what they say. If you're concerned about the outcome see a supplier you don't know.
Should any big kids go through it, or you wish to sell, you may well have problems.
Regards Rodders