Since an army's strength is represented by a CR score, you can balance armies against each other using the guidelines for CR in the Pathfinder RPG Core Rulebook. For example, two CR 9 armies should make for a relatively even battle, but so would a CR 9 army against three CR 6 armies. For War of the River Kings, the assumption is that the PCs' army will consist of a CR 11 army overall.

The Battlefield

In most mass combats, the battlefield shouldn't impact either army. But sometimes a battlefield can decide the outcome of a war.

Advantageous Terrain
Generally, if one army occupies a position of superiority (such as being atop a hill, wedged in a narrow canyon, or protected by a deep river along one flank), the defending army gains a +2 bonus to its DV.

Ambush
In order to attempt to ambush an army, the entire ambushing army must have concealment. The ambusher makes an Offense check against the army's DV—if successful, the battle begins but the defending army does not get to act during the tactics phase. Otherwise, the battle proceeds normally.

Battlefield Advantage
If an army is particularly familiar with a battlefield, it gains a +2 bonus to both DV and OM.

Fortifications
An army located in a fortification adds the fortification's Defense score to its DV. A city's Defense is determined by the types of buildings it contains, as detailed in Pathfinder Adventure Path #32. If you aren't using these rules, a typical fortification increases DV by +8.

Battle Phases

Mass combat generally takes place over the course of three battle phases—the Tactics Phase, the Ranged Phase, and the Melee Phase. A phase does not denote a specific passage of time, leaving you as the GM the latitude to determine how long any mass combat takes to resolve.

Tactics Phase
During the Tactics phase, each army selects which of its tactics it will use during the battle. Each army's leader makes a Profession (soldier) check. Starting with the lowest result, each leader reveals the tactics and strategy track he has chosen. The best result reveals last.
During the melee phase, Strategies will always be revealed in the same order decided here for the rest of the battle.

Ranged Phase
The Ranged phase typically lasts for 1 round, although the battlefield's shape and other conditions can extend this duration. During this phase, any army with Ranged capability makes an attack against an enemy army. Armies without Ranged capability cannot attack during this phase.

Melee Phase
The Melee phase begins as the armies involved finally clash—this phase continues until one army is defeated.

Mass Combat Quick Reference

The following summarizes the key rolls in mass combat.

Offense Check = d20 + OM

Damage = Offense check result - defending army's DV + attacking army's damage mod

Morale Check = d20 + leader's Cha mod + morale score

Strategy Track

During the Tactics phase, and each round during the Melee phase before rolling each Offense check, an army's commander must select a strategy from one of five options on the strategy track. Strategies adjust the army's DV, OM, and damage modifier (which is added to the damage dealt by the army but not to the offense checks themselves). Adjusting an army's strategy one step in either direction is automatic; if the leader wants to adjust strategy more than that in 1 round, he must make a DC 20 Morale check. If he succeeds, the army's strategy changes to the desired level, but if he fails, the army's current strategy doesn't change at all.

Attacking and Taking Damage

In mass combat, it doesn't matter who goes first, since in the game it's assumed that all attacks happen simultaneously. Each army makes an Offense check by rolling 1d20 and adding its total OM. This result is then compared to the target army's DV.

Attacker's Offense check equal to or less than defender's DV
Attacker fails to damage the defending army.

Attacker's Offense check greater than defender's DV
The attacking army inflicts damage on the defending army equal to (the result of the attacking army's Offense check) + (the attacking army's damage mod) - (the defending army's DV) - (any reductions to damage from tactics or other abilities).

Natural 20
If you roll a natural 20 on your Offense check, you automatically deal at least 1 damage to the army, even if the result of the roll is lower than the enemy army's DV.

Natural 1
If you roll a natural 1 on your Offense check, your army cannot make an Offense Check during the following round.

Rout

If at any point an army's hit points are reduced to a number equal to or less than its CR, it immediately flees unless its commander can make a DC 15 Morale check. If this check fails, the army scatters and retreats from battle. When an army flees thusly, the enemy can make one final Offense check to get a parting shot before the army escapes.

Multiple Armies

These rules can also serve in battles where multiple armies clash. In such battles, when you make your Offense check, you choose which enemy armies you're attacking and apply damage appropriately—you can change targets each round as you wish—these rules don't take into account complexities such as movement or location, after all!
When multiple armies are on the field, any XP they receive is shared between them. If equal XP shares aren't possible, the lowest CR army receives any extra that remains.

Victory and Defeat

An army is victorious once all of its enemy armies are destroyed or flee the battlefield.

Victory
A victorious army's hit points remain at the level they were at when the battle ended (minimum value equal to the army's CR). If the opposing army was defeated and not merely routed, your army receives XP equal to the defeated army's CR and your kingdom receives an amount of BP equal to the defeated army's (CR+Invested resources) divided by 4. Finally, make a Loyalty check against your kingdom's Control DC. If you are successful, your army can either learn a new Tactic or increase its morale by 1 (maximum of +4).

Rout
The army's hit points reset to a number equal to the army's CR, and its morale decreases by 1. Before this army can fight again, you must make a successful Loyalty check against your nation's Control DC during your nation's Upkeep phase.

Defeated Army
Although there are certainly a few survivors if an army is reduced to 0 hit points, those few survivors are so demoralized and wounded that the army cannot recover. It must be replaced with a new army. Every time an army is defeated, increase the kingdom's total unrest by 2d4.

Leaders and risks
Leading an army is not without risk. There is a 50% chance that the leader of a routed army is captured or killed by the enemy. The chance increases to 75% if the army is defeated. If the leader is a PC, there will be an opportunity to attempt to escape capture/death in a round-by-round encounter. The tactical situation will be substantially in favor of the victorious army.

Recovery

An inactive army heals back to its full hit points after a single month, but often, you'll need to restore your army to full fighting potential much more quickly. Each day that an army spends at rest (no movement and no battle), it heals hit points equal to its CR. Once per day you can also restore an additional amount of hit points to one of your kingdom's armies by making a successful Loyalty Check against your nation's Command DC. With a successful check, the army heals an additional amount of hit points equal to its CR.

Conquest

To conquer an enemy hex, an army must remain in the borders of the hex for a full month. If the army has not been defeated within the month, the enemy kingdom loses the hex your army occupies and increases its Unrest by 1d4. All special resources remain in the hex and any Cities in the hex become Towns. The conquering army may then claim the hex like any other new hex during the Improvement Phase. If claiming a Town, the kingdom must roll a Stability check (DC = Command DC) and increases its unrest by 2d4 if that check fails (see Special Resources).

Alternatively, an army may raze enemy structures to the ground. To do so, an army must remain in the borders of the hex for one full day (in plains or grasslands), two days (in forests or hills), or three days (in mountains or swamps), without moving or entering battle. The enemy kingdom then loses the hex your army occupies and all enemy improvements in the hex (farms, roads, cities…) are removed. You may then claim the hex normally during the Improvement Phase. Razing an hex doesn't count as rest - an army razing an hex doesn't recover any hit points for the day.

Player Characters in Battles

As an option, you can have the PCs face battles of their own just before or even during a battle in which one of their armies clashes with the enemy. For example, the PCs might attack an evil necromancer and fight their way through his tower to confront and defeat him while their army battles the undead horde outside.

Alternatively, the PCs could use a few potent spells (such as control water, earthquake, cloudkill, and so on) to adjust the battlef ield condition to their favor. These possibilities allow the PCs to use their characters to directly affect the outcome of a battle without actually forcing the characters to "sit out" on an adventure opportunity by personally commanding an army.

If the PCs win their battle or dramatically affect the battlefield with magic, increase their army's DV and OM by +4. If the PCs lose their battle, penalize their army's DV and all OM rolls by -4. At your discretion, the PCs' failure or victory can have other effects on their army as well, such as granting temporary bonus tactics or starting the war with adjustments to one side's hit points.

Sample effects of PC intervention :

Lyre of building
Playing the Lyre of Building for at least an hour prior to battle raises the DV bonus from fortifications in this location to +3 if it was any lower. Striking the chords during battle when fortifications are already present increases the fortification bonus to DV by 1 for 3 rounds and negates the fortification-destroying effects of the Siege weapons resource for that duration.

Inspire courage + Clarion call
Bonus to OM and morale equal to the bard's Inspire Courage bonus.

Hallucinatory terrain
If an army fails its morale check (DC10+1/2 caster level), it loses its Battlefield Advantage bonus.

Witch's healing hex
An inactive army with a healing witch (or another healing ability capable of being used freely on the entire army every day) heals back hit points equal to twice its CR every day. This bonus is granted once no matter how many healing witches are available.