I think the reason you find it difficult to put lots of dragons in the fortress is because dragons work better solo. At the very very very most, I'd put two adult (or better) dragons plus a nestfull of wyrmlings, and that only applies to certain colors, like silver. Other dragons might have a max of only the mother and babies. Or even a max of just one.
But to be perfectly honest, you don't usually NEED more than one dragon. One Dragon is more than plenty, if you use the dragon right. Since this is a huge fortress, give the dragon minions... kobolds are traditional, but with evil dragons, anyone that can be bullied is fair game.
If you use wyrmlings, may I suggest that there be a limited number of them... say six or so, and you NAME THEM ALL. Name each wyrmling, give them each a personality... I find that pretending a wyrmling is a lot like a kitten works well-- but then, the kitten my house just got is a mean little bugger of a cat. Go through great lengths to keep these wyrmlings alive... even white wyrmlings at CR2 can have a decent lifespan if played right. Use that speed advantage! Never sit still long enough for anyone to get a full attack off! Guerilla tactics! There may not actually be a lot of wyrmlings around, but your players will think there are!
And if you give each dragon identifying marks and personality traits, they become nemesis to the players little dungeon romp. It's hard creeping down passageways when "Wyrmling A" is having fun playing his own version of a RTS with you as the opposing force using Mommy or Daddy's kobold minions for troops. "Wyrmling B" might hang around dark corners waiting for just the right moment to pounce and then fly away. "Wyrmling C" has a little extortion racket going on, backed up by all those kobold traps... want to get through the HALLWAY OF DOOM? Gold now please, that will do nicely in my growing hoard. Lower the drawbridge? Sure... for another donation. Bleed 'em dry, and if the little dragonet is cautious enough, no danger to him/her!
You can also do draconic theming. I saw some neat custom spells in House Rules... like one ruleswise identical to magic missile, but instead of appearing as bolts of light or whatever, looking like tiny flying dragons of energy. Sepia Snake Sygils can be retouched to work with the dragon theme. Decorations go a long way.
There's a lot you can do with a small number of dragons... and don't forget the big one at the end. Always good for a climax. And BE CERTAIN to structure that final room so it is tactically advantageous to the DRAGON, not to invaders. So there should be flying room, and high alcoves, and places a dragon could ambush from... that sort of thing.
Be nasty. Dragons are smart and dangerous. While they are physically fearsome, it's not the HD that gives them strength... it's the fact that they won't fight to their own deaths if they can help it, they tend to use their advantages (like Blue dragons flooding their dwelling places with water so as to better shock their foes, white dragons using lots of ice and fog, both of which are no hindrance at all to the dragon... all dragons have their own little ways of being nasty to invaders...) and it's hard as hell to hit them, do to that astounding speed. Let the dragons be dragons! Make your party WORK for that treasure! Let them remember the NAMES of the dragons they slay... rub their noses in the fact that dragons are mean little buggers who don't play by the rules adventurers prefer monsters to play by!
B.A.D.D. man! Bothered About Disposable Dragons!
