I'm acctually working on this exact thing myself. I'm thinking about having the highest commander of the troop represent the troop as a whole for everything except attack/defense and hit points. And of course with some alteration to things like Stealth checks. I've divided the units into the following troops:
Light Infantry, Heavy Infantry, Artillery, Mounted Artillery, Light Cavalry, Heavy Cavalry, Mobile Siege Weapons, Stationary Siege Weapons, and bases (e.g. camps, towns, ruins, castles). But I want to simplify it somewhat, so I'm thinking having 3-4 kinds of attack and 3-4 kinds of defense. But I haven't worked out the kinks yet.
Of course, I'm doing things medieval style. You didn't mention in which era your campaign is set. If it is contemporary or futuristic, you don't need to worry much about large scale battles, since most battles today are fought with small elite units, much like a standard adventuring party. If there's any other units fighting closeby, you can just narrate the action.
Concearning the emissary, will they act as bodyguards or more like caravan guards?