Mass combat is tricky with a game that is focused on individual characters and their stories. However, war and battle are extremely dramatic situations that can add a lot of excitement to a campaign and really drive a story forward. With that in mind here are a couple methods for handling mass combat in your game.
Have the battles fought in a war happen away from or at most, close to the characters, but do not have the characters directly involved in the battles. This allows you to describe the ebb and flow of the war, but not have to deal with a massive battle that the characters cannot control.
In this instance, the characters are directly involved in the larger battle. However, instead of just having them in the ranks, they should be assigned objectives that they either complete alone or at most with a small squad of soldiers. For a truly large battle, they could have several small objectives to complete over the course of the day (e.g., the party is tasked with taking over a hill on the edge of the battlefield being used to shell their army, then they have to destroy a small bridge over the nearby river to prevent the enemy from using it to bring in reinforcements, and finally, after the battle is won, they are involved in the race to catch the enemy leader before they can return to their stronghold and raise another army).
In the final instance, your players are the commanders of the armies. This one requires a more formal system as they give out orders to their units and you work together to determine the success or failure of their plans.
A fully fleshed out Mass Combat system involving the characters as commanders is outside the scope of this ruleset. A mass combat system that ties into this ruleset is a likely future optional ruleset or addition to a specific Settings Pack.