This may need confirming, but in my personal exp of the later game;

when I've taken a complete region I generally keep only 1 city exclusively for horse, 1 city exclusively for soldiers and 1 exclusively for archers, every other city has all their fighting buildings destroyed and used only for trade.
I can then move any growing cities population to the war cities, which are then trained up, and any other city that rebels finds itself only able to train peasants.
Also if one of my war cities rebels, they can only train 1 type of fighter which is easier to fight against. ( unless they have a city of wardogs; which happened before - oh my )

( note: I have found if a city rebels quickly after being taken it will manage to recruit full stacks of all types regardless of if you've destroyed the training buildings. I can only assume they were hiding in the peasants houses, shields and swords used for coathangers )

Each region ( eg. Spain or Africa or Europe etc) has its own 1 full stack to move around killing rebels and to besiege any city I allow to rebel.
then all the rest of my armies are on my front line, and I have a regular train of recruits travelling the map to the front line.
Each city only has peasants to garrison and if it requires more than 5 peasent units - let it burn.
I also use Best capital Map which always shows the best placement of my Capital to keep down the dist. to cap penalty.

hope this helps.