Go to descr_strat, almost at the bottom of the files, right below the list of rebels settlements, you will see entry like this:
character sub_faction aztecs, Coanacoch, general, male, age 22, x 7, y 75 army
unit Native Warriors exp 0 armour 0 weapon_lvl 0
unit Native Archers exp 1 armour 0 weapon_lvl 0
unit Native Warriors exp 0 armour 0 weapon_lvl 0
unit Native Archers exp 0 armour 0 weapon_lvl 0
unit Native Warriors exp 0 armour 0 weapon_lvl 0
unit Native Archers exp 1 armour 0 weapon_lvl 0
unit Native Warriors exp 0 armour 0 weapon_lvl 0
unit Native Archers exp 0 armour 0 weapon_lvl 0
That's rebel army in garrison in vanilla grand campaign, easy to spot because of the 'sub_faction', which is for rebels only. just copy all those armies from the original geomod descr_strat crusades to your own, and the rebels armies will be back.