I don't think adding the Dragons as an actual units is a good idea.
I believe my original idea of representing the Dragons via Ancillary's for each of the riders would be best, for example Balerion for Aegon giving him + Troop Moral & Hitpoints. The Ancillary's would be powerful and give the riders a much needed edge when they clash with House Targaryens numerous enemy's in Westeros, and naturally each of the riders would have 10 Command. (Aegon, Visenya and Rhaenys) I'd also start House Targaryen with control over most of The Crownlands, as The War starts when Aegon lands in Westeros. (If they only controlled Dragonstone, they would never get anywhere under AI control) When Aegon landed he sent Visenya and Rhaenys to subdue the local lords; Rosby yielded to Rhaenys and Visenya took Stokeworth without any bloodshed. The Darklyns of Duskendale and Mootons of Maidenpool did put up a fight but were easily beaten. So Rosby, Stokeworth, Duskendale and Maidenpool along with a fort named Aegon's Landing that could maybe turn into Kings Landing via a script of some kind? (Kind of like how Wolfs Den turns into White Harbor) Aegon would also have Dragonstone and Drfitmark.
The seven rulers at the time were:
Torrhen Stark, King in the North.
Ronnel Arryn, King of the Vale, a young boy whose mother, Sharra Arryn, ruled as Regent.
Harren Hoare, King of the Iron Islands and the Riverlands.
Loren I Lannister, King of the Westerlands.
Mern IX Gardener, King of the Reach.
Argilac Durrendon, King of the Stormlands.
Mariya Martell, Princess of Dorne, a blind, balding woman of 80. Known as the Yellow Toad.
Certain locations such a Harrenhal & Aegon's/Kings Landing would need to be added. House Mudd would need to be removed also as they have died out, The Riverlands should also have low public order.