Controlling Armies?

Star Wars d6, the old West End Games version, had combat rules that scaled from individuals up to Deathstar-scale seamlessly.
You could do space armada battles pitting the Rebellion Irregulars against an arrayed Empire fleet, if you had 8 hours to set aside.
It helped that the combat rules also scaled multiple individual efforts into a single roll.

Here's an example-
A band of 40 fighters combine to attack as a single force, and receive +24 to hit, +24 to damage, but only make a single roll.
If they break into 4 groups of 10, they combine to make 4 attacks at +14 to hit, +14 to damage.
Attack roll is against DC of the average AC of the opposed force, modify DC by various situations that give defensive advantage.
For every point over the DC, attackers connect with one defender, do some damage typical of their weaponry, just use average damage (1d8 weapon does 4).
Force HP is the sum of unit HP, so each turn subtract HP of damage x point over DC from Force HP.

That's a little abstract.

The men of the woods stand guard at the main force's flank. Average fighters, these men all trained at their village in the forest for a year in preparation of this call to arms. Their armor of hardened leather doesn't interfere their agile defense.
Abruptly, a brace of crazed outlanders charge their position at the flank, striking without warning and in a flurry. The small raiding band swing heavy axes of massive beast fangs lashed to hafts. Though only a fraction the size, the armored and furred raiders strike without hesitation, no shortage of woodsmen to attack. They strike and woodsmen begin to fall as trees.

Group of 40 fighters, the Wood40, have 400 HP, AC 15.
Get hit by group of 10 barbarians, Fang10, roll (11)+14 is 25 vs. DC of 15 from AC.
Fang10 have battleaxe, 6 damage.
10 hits (25-15) of 6 damage is 60+14, so Wood40 is down to 326 HP, only 33 fighters remain.

Undaunted, the woodsmen strike back with practiced swings of gleaming new longswords, provided by their seige commander. The outlanders sneer in the face of this riposte, but the woodsmen number so many. Wound after wound is drawn through thick furred quiltwork plate as numbers push back. With so many attacks, the woodsmen push their 4:1 advantage, only the press of bodies keep them striking down all the outlanders down.

Fang10 have 120 HP, AC 18
Wood33 roll (11)+21 is 32 vs. DC 20 (AC 18 + 2 Morale).
Wood33 have longsword, 4 damage.
12 hits (32-20) of 4 damage is 48+21, so Fang10 is down to 51, only 5 barbarians still standing.

Suppose, though, the woodsmen carry magic shields, hewn from old growth nurtured by generations of their village for just such a struggle. The enchanted shields block blows, but the heavy bone axes still find a way above, below, and around.

Group of 40 fighters, the Wood40, have 400 HP, AC 19 (Dex + armor + Shield).
Get hit by group of 10 barbarians, Fang10, roll (11)+14 is 30 vs. DC of 19 from AC.
Fang10 have battleaxe, 6 damage.
6 hits (25-19) of 6 damage is 36+14, so Wood40 is down to 350 HP, now 35 fighters remain.

The seasoned outlanders have raided since early in the war always striking early the confidence of survival worn like a shield. The woodsmen counterstrike but the furred interlopers withstand more swords than woodsman can fit around each broad armored shape.

Fang10 have 360 HP, AC 18
Wood35 roll (11)+21 is 32 vs. DC 20 (AC 18 + 2 Morale).
Wood35 have longsword, 4 damage.
12 hits (32-20) of 4 damage is 48+21, so Fang10 still has 291, still 9 barbarians preparing for another round of hacking.

+++

For this approach to work, the forces need to be largely uniform, extremely generic. Average HP, average damage, same weapons, same armor, same training. In the above example, 5th level barbarians attack 1st level fighters and illustrates how numbers, experience, equipment can affect the checks.
The actual bonuses by numbers from Star Wars were so:

Number in Force	Bonus
2	+3
4	+7
6	+10
10	+14
15	+17
25	+21
40	+24
60	+28
100	+31
150	+35
250	+38
400	+42
600	+45
1000	+49
1500	+52

As you can see, as the forces become extremely large, the attack roll becomes less and less relevant. The equipment is less and less relevant. It just turns into giant waves of soldiers wailing away on each other.
You may have noticed in the above example the Wood33 and Wood35 had a +21 bonus, while Wood40 started with +24. As the forces get whittled down, their bonus shrinks whenever they fall below the number on the chart.
In the d6 system, each force needed a discrete commander unit to coordinate any number of forces. The quality of the commander determined what size of force they could control. Forces would be opposed, and a commander could direct his units to attack the opposing commander directly. Targeting the opposing commander would disperse the force and remove them from the field as units fled the dispatch of their commander (That's why you have a Lieutenant Commander to rally over your body). Call it a Leadership or Command Feat or skill check for (Tactics), etc. This is in 3.5 language.

At this point, advice for army battles.
Don't roll them out mechanically. It takes forever, and you don't end up with that many surprised from amazing luck. This is why forces used to line up and press overwhelming numbers. Army battles were, historically, just round on round of men with sharp things wailing on each other. There are generally no scrappy underdog bands of ragtag losers who conquer their way across the melee.

Wars are massive actions, involving monumental numbers of combatants. D&D is generally not scalable to large warfare. Campaign wars should be orchestrated by general outline, almost like a sandbox.
 
I would include planned set pieces, movements, and crises that take place at set times or intervals. Each is intended as a beat of the game to be experienced by players-- it's important to remember the war should serve the purposes of the party, so your PCs will need to experience it from their own perspective.

Set pieces are any terrain or area where you would want PCs to appear. Sun Tzu says to pick your battlefield, so the fog of war is an easy way to convince your party that amongst the larger battle, they find themselves in a particular setting. Set pieces are ruined buildings, devious traps in the woods, the ramparts of a castlement. If players had a view of the wider map, set pieces would probably be represented as obstacles or difficult points for large units to manage.

Movements are planned actions of forces. In any war scenario, there are going to be NPCs commanding an opposition, as well as Allied, forces. Generals have a plan when they are entering the field. Commanders & Captains are enacting that plan. The movements can serve as timers, countdowns, or obstacles to the PC. If the party needs to get to a flanking position before the main infantry marches, that's a timer. If PCs must repel castle attackers until the cavalry arrives, that's a countdown. If the PCs happen to have camped where an enemy is marching, they'd encounter advance scouts.

Crises are any planned battle that the PCs will witness. These can be in set pieces or part of movements. The Crises could have a number of outcomes, good/bad/middle. These outcomes should be generally known, and actions of the PCs will resolve the scene. These scenes, assembled into blocks, are a way the PCs could have some tangible outcome on the war. If the PCs can stop the invading hordes only if taking a last resort, fighting to the river dam and flooding the field, that outcome should require success or a path through a number of prior crises, each an obstacle for the PCs.

That's a lot of musing and doesn't really speak to how you might make up rules.
I guess generally I would do as much rolling and random-outcome generation in pre-work. The old d6 system could account for truly galactic confrontations, but the dice rolling was tedious. Imagine counting 15d6 of fireball several times every round, for every combatant. War scenes just can't achieve the same spontaneity of smaller party scenes... or they can, but the flexibility you need to have for your war unfolds comes at a cost.
 
I think generally, you can actually use the generic D&D rules. Just imagine each force or troop is a single PC or monster. D&D started as a miniaturization of war games. HP is an abstract measure of vitality, because it used to represent discrete units of a larger force; a column of tanks or a troop of infantry. 1 unit = 1 hp.  Rolling d20 for randomization was always to be a random influencer on a unit's attack capacity - Howitzers with skilled +12 operators are just elven rangers in a different setting.
From a purely practical perspective, running army / war scenes generally requires quite a lot of space for topography, and not all gaming tables are equipped for 3D landscapes or huge floor mats.

Hope this helps, it is homebrew after all so it should work best for what you want from it.