I've got a production line of military dwarves working ok, I only have ten civilians, about 15 front line troops, about 15 second line troops who only fight the odd enemy that wanders past the front line troops, and the rest are newbies inside the civilian area of the fort. The front line troops are all legendary shield users and aren't (AFAIK) getting hit by the the fireballs, they are walking into fire on the ground started by them. It's hard to tell because no message seems to come up for that and they just eventually bleed to death. They also don't go to the hospital either for their wounds it seems.
I've tried building a limestone road outside, and it caught on fire and burnt down leaving some dead dwarves lying on furrowed soil. I tried building a long underground entrance, which works ok, mainly because other beseiging races normally flush them out before they get to my dwarves. I've tried flushing them out with my crapper axedwarves with mixed results: works ok for individual thieves but multiple ambush squads can sometime kill the axedwarves and rush to my entrance. I haven't tried marksdwarves.
I haven't had any problems with Nightwings for a few forts. Generally you can deal with elite flying bowmen by killing enough of their accompanying squads, causing them to leave the board. I've found the worst thing to do here is use marksdwarves, they'll tend to shoot the squds while getting shot themselves and don't kill stuff fast enough. Melee squads get the job done usually.
I have war elephants riding polar bears, which doesn't make sense either. They all end up dead regardless.