Not being a rules lawyer, (and not having needed this method in a while), when there is a massive military conflict, I run the battle in a very abstract, narrative fashon. The PCs get the actions as a normal D&D combat against a handful of assigned "skirmish" foes. For the companies of other troops, I roll d% for the enemy, and the players do also for their allies. The higher roll and difference bewteen the two determines the sway of the battle. Then I describe what is happening on the field between each players turn. I use the PCs skirmish results to determine the outcome of the whole battle. If they defeat their assigned skirmish foes, say 20 of them, and the rolls are all going in their favor, when the 20 are felled, their allies are also triumphant. If the rolls were in the favor of the opponent, then the PCs get assigned more "skirmish" foes. If the rolls have been consistantly in favor of the enemy, and the PCs are getting beat, so are their allies. Rinse and repeat until one side retreats or is slaughtered!
Like I said it is very abstract, and leaves a lot to the DMing to adjudicate. But, the positive is that there are no rules to memorize.