Hello and welcome!
Large scale battles can be great fun. DnD 3.5 has a supplement book,
Heroes of Battle, that give some rules on running sieges and mass combat.
Notes on structure:
Most RPGs generally tend towards a small squad-based focus on action. You'll have a party of PCs each fulfilling some party role and they'll do exploits together. If you keep this structure, you can have them perform as a modern commando unit. They're the ones sent in to accomplish various elite missions, while the regular army of grunts keeps the enemy occupied elsewhere.
The problem with the squad-based adventure is one of scale. You must scale down their operations to something small enough that an adventuring group of people could realistically do. (Otherwise, if they're taking on superhuman odds and winning all by themselves, your players may start wondering why they even need the friendly army at all.)
Possibilities:
- Sabotage a weak point in enemy defenses, like starting a fire at a thin part of the city wall
- Assassinate an enemy general
- Intercept an enemy spy carrying volatile information about your army
- Carry out a false flag operation (do evil nasty things while pretending to be your enemy, so local peasants hate them) like poison wells, salt fields, rape and kill and steal and pillage
- Carry out a humanitarian operation (do good lovely things to give your army greater support with the local peasants) like cure diseases, provide food and shelter, and relocate refugees to safety
- Steal enemy plans or sabotage key enemy supplies, like putting rotten oats in their warhorse feed bags
- Carry out raids and feints to disorient the enemy and draw their main strength away from your army's intended real attack point
Another adventure structure you can use is to have PCs leading a column of the army, tasked with a more large-scale mission. These will probably do well with the mass combat rules of whatever system you're using - but bear in mind these will be somewhat different from individual combat, and so either you or your players will have a little acclimatization to do. (In DnD it's almost all on the DM - the PCs are still told to make rolls against familiar stats and skills but the DM is the one handling how they operate slightly differently.) These can afford to be much more grand, because you're talking about leading an entire section of the army.
- Destroy an entire enemy fort
- Annihilate, rout, or disperse an entire enemy division
- Take and hold a key location on the battlefield, like a specific high ground vantage point so your friendly siege can deploy there and enemy siege is captured or destroyed
- Clear and secure an entire highway providing supplies for your army or denying supplies to the enemy army
- Block a mountain path or city gate or river bend so the enemy can't use it anymore
Division-level warfare also comes with several problems that you can tweak to give a real sense of battlefield logistics. Generals also have to worry about supplies, which PCs can generally carry with them. A large number of soldiers needs sleeping tents, food provisions, medicines, ammunition, and odds and ends for breakages. (One of the main morale boosters for coalition troops in Iraq was wet wipes sent from home. It's hard to stay clean and hygienic when you've only got dry paper to clean with.)
Troop morale is also very important, and a number of psychological factors play into this. Some generals will even pick easily-won engagements that have little or no tactical value at first, just to show their troops "Look, you can do this!" and so when the crunch comes later, they'll feel more positive about it. When two large bodies of soldiers meet on the battlefield, you rarely get a fight-to-the-last man scenario. More likely, whichever side has the stronger will to stay on the field will prevail, and the losing side is usually the one that people run away first. You can regroup after a bad battle and reform your ranks, but it's a situation most would rather avoid...
Loyalty is another factor that PCs in a squad rarely have to worry about, but which is important in large scale battles. Leaders need to know why their men are fighting, and to keep them motivated, and to keep them fighting for their side. If the enemy army has made use of conscripts by holding their women and children captive, you could disintegrate their entire fighting force overnight by liberating their women and children instead of fighting their armed men on the field. Likewise, if you have a column of River Province folk under you and River Province has already been liberated, you're going to need greater incentive to keep those folk fighting instead of returning home to their households and families. PCs may find themselves in the moral grey area of punishing deserters and dealing with politicians, while still trying to stay the good guys and heroes of the piece.