@Tad, you basicly expanded that for me, that was more or less what I was going to say. My idea was more to let the players run standard adventures for 5-10 levels (assuming D&D, but whatever) at level 5 start hinting at the comming war, armies moving, quests to recon the enemy lines, towns reloacting etc.
If the players seem interested, let them move towads an active role in the military war machine, taking missions for the crown or what not. As the war commences, have them in a position of influence for the kings and generals etc. Let them choose where to go and what to do, if they choose to return to the kings and generals they would have a chance to influence the war strategicly, or they could continue to run missions behind enemy lines or out side of communciation with the generals, taking more of a tactical approach. Finally they might decide this whole war thing is for the birds and go find someplace safer to adventure until it winds it self down...
This approach requires quite a bit of work though, as you have to have some level of planning for each possiblity, thus the difficulty. That doesn't even get into the 'feel' of the war, which would just be the GM's talent to bring this type of world alive...
-Scott
**modified to fix major spelling error