I start with a courtyard that has a 3 tile ramp down to a drawbridge into the courtyard. Later (in time for the second dwarven caravan at the latest) I expand the entrance to a serpentine dug caravan entrance path and make a roof over where the previous entrance was. The entrance path has another drawbridge at the end and a replacement set of ramps down to it.
The above means I don't use stairs but ramps in this case (when channeling out the courtyard initially ramps are formed naturally, but I remove them before putting up the roof (I think conversion of a sun exposed ramp into a floor removes the sun exposed trait, and thus makes those tiles unsuitable for grazing/overground farming if channeled away later).
Basically:
wwwwwwrrrwwwwww
wwwwwwbbbwwwwww
wwwwwwbbbwwwwww
w.............w
w.............w
w.............w
w.............w
w.............w
w.............w
w.............w
w.............w
w.............w
w.............w
w.............w
wwwwwwwdwwwwwww
wwwwwww.wwwwwww
wwwwwwwfwwwwwww
wwwwwww.wwwwwww
wwwwwwwDwwwwwww
wwwwwwwwwwwwwww
where:
w=wall
r=ramp
b=drawbridge
d=door
f=dwarven footbath (to wash away blood, etc)
D=down staircase
The door is there from the beginning, where it's needed to keep undead out if they attack during the first summer.
Down below I have a tunnel with an airlocking pair of drawbridges and cage traps in between.
Yes, you can roof over fortifications the same way as you can roof over walls. There is a caveat, however, in that BUILT fortifications do not have an integrated roof, whereas CARVED ones do. This has two implications:
1. You shouldn't be able to walk on top of a built fortification, since there is no floor there.
2. If you forget to build a floor over the built fortifications critters can get in diagonally from above. At least flyers (including those pesky Keas) can, but I'm, unsure if that's valid for climbers as well.