Ok to forgo the details because I would rather not get into it.
How exactly would a huge fight go down PC would control a army of 20-40 npcs they can only give orders they don't roll for them and the npcs can act on there own.
I would rather not roll for them myself because this would leave the player with one turn every hour.
I thought of a moral system where the pcs troops do well in combat depending on how well the pc does and to top it off Have it kinda like an army vs army rather then a individual vs individual.
A group of 6 normal solders add up there max HP, AC, TH, and DAM then use them to do army combat
I'm looking for any input
As far as I know there may already be a system in place for this.
3.5 had Heroes of Battle, which includes a couple chapters of good advice on how to construct a mass battle (essentially as an 'event-based adventure') as well as rules on morale, battlefield terrain and lots of other stuff that would be useful in the situation you describe.
The main thing to bear in mind is that any time a combat is taking place entirely between NPCs, you can save a huge amount of time by simply describing the action rather than bothering with initiative, attack rolls, etc. Imagine it as a cut-scene from a movie, or - alternately - as a report from the battlefront to the general:
"While you guys were battling the enemy griffon-riders, the Principality's 3rd Heavy Infantry was being bloodily repulsed from Watcher's Hill. Your side is doing very badly over there. On the other flank, the fog you created allowed Gorwain's cavalry to catch the goblin archers off-guard: the few goblins that weren't trampled ran to the river and are swimming for their lives."
I own the book in question, and I cannot endorse it and your subsequent suggestions highly enough.
Exalted has a system where you "wear" your soldiers, i.e. They boost the character's stats. It makes for a very heroic system, but would likely not work well in PF.
in 3.5 you also had the mini hand book which basically stated you treated each army as one unit with a combined hit point total and damage total. They used a single AC (we're assuming all soldiers are basically the same). and each army rolled their attacks each round. if the attack roll beat the enemies AC, damage was dealt from every unit. Basically
40 Units (A) +1 to hit 7 hp AC 14 1d6
40 Units (B) 0 to hit 9 hp AC 16 1d8
Unit A wins their initiative and so attacks first. they roll 11 total so the entire group misses. Unit B rolls a 14 so they hit. they roll a 4 for damage so its 40*4=160. they have 7 hp/unit so 160/7=22 with a remainder of 6. So unit A has 18 people left though one of them is at 1 hit point. This continues until a victor is decided. and yes it makes turn arounds difficult. Thats how battles are.
I was thinking the same where an army's to hit is relevant to Moral and Moral is generated through a PC Heros actions.
Thank you All
We have always played big battles using rules similar to Axis & Allies, but with more kinds of dice. But we've always designed the big battle to be one where the PC party is a special-ops team and they have a specific task that they perform under standard PF (or 3.5) rules. The execution of their task provides an advantage to one side or the other and is intended to be the pivot point of the battle.
But the honest answer is that in general we simply avoid large battles in PF. The PF rules are not suited for large armies, and it is usually best not to try to have your characters (who have been built around those rules) suddenly at the mercy of rules they are not designed to execute.