There are two different matters here:
1 - Fixed garrisons: once you have defined the model and unit, in the scenarios you just fix it in the concern region (code 999 in Column G). This is the best. In such a way, those units won't move unless attacked (i.e. after the city is stormed).
2 - The second point is trickier but feasible. We may define some events where, based on loyalty level, a certain unit in the region is eliminated and replaced by her counterpart from the other side. This is feasible, but to make things work correctly, it would mean you have to define as many units (for each side) as there are concerned cities in the scenario... not a big deal, around 50-60 cities, that many original units... unless Pocus has a better idea