If you've got access, look up the rules for Kingmaker. The relevant books are River Runs Red for the rules on cities and income, and War of the River King for rules on Mass Combat. It essentially forms armies into single units at a base size of 100 soldiers, generally Warrior 1, which is the generic combat NPC class, at level 1. However, some of the factors are a bit off... It costs 2 BP (ie, kingdom-gold) to equip an army with masterwork weapons. According to who you ask, that's 500, 2,000, 3,000, or 4,000 GP.
BP is a variable resource, apparently. It's generated by cities and farms and whatnot and usually kept within the kingdom, which is fine.
You can drop adventurer's wealth into the BP pool at 4,000GP:1BP.
You can withdraw BP from the pool and into the adventurer's pocket for 2,000GP:1BP
Thus many sources say, 'If you're not using BP, just use 3k gp as base price instead.'
The Kingmaker book also says that if you're not using BP, then upkeep is base 500gp per 1BP.
However, BP is very vague, as it's 'general wealth' and assumes that if you build a city on every scrap of land, that the citizens will be prosperous enough to buy their food... from... somewhere? I'm likely to replace BP with more variables on things like 'This farm doesn't produce 1BP, it in fact produces 2 units of food.' So, the player won't be able to completely muddle the system. Similar for ore, stone, etc, but cities will be able to take raw resources and produce gp and items.
Kingmaker rules for cities are generally very vague and just look like stand-in rules while they think of more accurate ones.
So I'm going to redo the rules on Kingmaker content in favor of something more homebrew balance, because it's otherwise kinda broken, but still use it as a base since I'll have a structure to build on.
In terms of Leadership and Kingmaker, mooks will be able to function as a lower-cost army, but of a limited amount, primarily meant to guard your person from being surrounded by an opposing army and just buy time while you figure out what to do. Cohorts will be able to assume leadership positions (treasurer, royal assassin, warden, etc) and lead armies, although random NPC will be rolled up to fill these positions as well, refreshed each month or so.
Mooks can still be used for conventional purpose once Kingmaker rules come in, like tending the wagons, tending vehicles, or sitting around town trying to earn spare cash or attempt production - level 1 mooks will be unskilled labor, but higher ranked mooks can be allowed to take specialty roles and try crafting or profession skills, allowing them to produce equipment, enchant items, or attempt to make gp by simply working the town. However, mooks are still pretty lame, and can't produce higher quality goods nor produce anything very quickly. But, I dunno, if you find piles of short swords, you could have the mooks enchant them to +1 and then resale them, or to hawk your loot to merchants and try and make a higher profit. I'm really not sure, we'll see what happens.
Keep in mind, this can be a lot of dice rolls. I'm very likely to port it off and make my own Python script to roll dice in bulk for massive mook checks, and most of them will fail. They are mooks, after all.
NINJA: Burned forts offer no loot.