ORIGINAL: eightroomofelixir
If I recall correctly, Turtledove mentioned some kind of outlaws were active in the Ozark Mountains around Missouri and Arkansas in the first book, but never elaborate it afterwords. Don't know if you are interested to put some partisans here.
I think bushwackers spawning in the countryside might be dealt with mostly through events - actual partisan hexes will be urban.
Roughly what I'm planning is to have the various insurgencies (Deseret, Congaree, Black Belt) modelled as sudden declarations of independence in 1915 within the US/CS (as I understand it, this will cause US/CS units in the area where this happens to move to the nearest friendly territory). Salt Lake City will be capital of the Deseret, Albany GA will be capital of the Black Belt, and St. Matthews SC will be capital of the Congaree. If the US/CS manage to crush the insurgents, then their capitals will be a partisan spawn-point which the US/CS will need to keep occupying troops in.
To actually switch the partisans hexes off the CS player will have to choose to open enlistment in the CS army to oppressed Confederate black people in an event firing in late 1916. This will have the effect of annexing the Black Belt and Congaree republics and switching off the partisan-spawn, as well as adding a number of infantry divisions to the CSA build-queue, but will also hit national morale and maybe MPP.
Turtledove makes it sound as though the Red Rebellion was widespread but the Congaree and Black Belt republics were the only ones named in the books - I think elsewhere in the south the CSA will just get a hit to MPP production and national morale, maybe unit strength. I'm not going to try to invent any Red republics not named already.
The US won't have any way of switching off the Salt Lake City partisan spawn and will just have to keep it occupied.
I think both the Deseret and Red rebellions should happen regardless of whether they are supported by the CSA/USA, but support should make each rebellion stronger. For example, if the CSA supports the Deseret uprising at a cost to MPP, then the units that spawn in the Deseret should already be upgraded to Infantry tech 1, and maybe some additional units should be formed. Similarly, if the USA supports the Red Rebels, then they should be upgraded to Inf Tech 1, and maybe have more (or bigger) units.
Elsewhere, probably all big cities will be partisan spawns in Canada, the USA , the CSA, and Haiti so you'll have to keep them occupied. This is mostly because it hurts the USA the worst, and the game needs things that hurt the USA for balance.