The wonderful thing about a chain of command, is that there's the rank and file, there's the head honcho, and then there are those important guys in the middle who aren't at the very top, but are very important and, most importantly,
potentially defeatable.
As for making them feel the war, I actually suggest against what the previous poster said: have them in the big battle at one point. Maybe that's when they're going after a lieutenant (good grief I spelled that correctly). Then you can do all sorts of fun stuff, like have mobs come at them in the middle of a fight. Oh man, you're not doing so hot, and you've almost beaten this enemy, but
oh hello there small troop of zombies I forgot there were a whole lot of you around here. Maybe set up a few random not-quite-encounters while they're out slugging it in battle; roll the die, see a five, tell the party to roll reflex for the fireball that just came roaring at them from elsewhere in the melee. See a four, pepper them with arrows. See a three, one of them gets healed. A two gets a few friendly NPCs - probably best if they're on the weaker side - to help them out. Nothing too damaging from said friendly NPCs, mostly have them assist with flanking and the like. But you get the general idea - make the war
interactive, so that battles aren't quite so simple as they normally are.
If you haven't decided the fort's fate, I suggest you let the players affect it. Maybe rig it so the lieutenant, for every round he's alive, has a negative effect on the Good Guy NPC; it'll help the party want to kill him as fast as they can. Or maybe send the party behind enemy lines; take out those evil clerics and stop the flow of undead! You don't neccisarily have to roll out the battle for the two NPCs, but set some vague standards for Things That Help (Kill the second in command in
x rounds) and Things That Hurt (Take to long to kill the guy, botch on your mission to disrupt supply routes). If the party does enough of the former and avoids the latter, they win! (Make sure to include their accomplishments, but throw in a few things they didn't do to add to the scope. You can even use this to establish other NPCs for the party to talk to and perhaps get a few delicious plot/quest bits from.
"Oh man, you're the guy who killed those enemy archers? They were hitting us big time!").
If you noticed there's a lot of mention towards events that would be timed (not in REAL LIFE time, though if you're
mean you can do that), it's because that's the kind of stuff that adds tension. If the players spend two hours aimlessly whacking some guy, it's not really that tense. If they know they have to kill him
right now, it pushes them to act a lot harder, and to really think about their resources before they use them. As a side note, in that kind of situation, 4e's power system
shines. They'll never be more glad to get that brief breather between combats to grab those encounter powers and pray they wouldn't have needed that daily after all. This could also really help the pacing of the encounters - maybe to get the second in command, they have to go through a large group of enemy peons; they know they have to go through them fast, but they ALSO know if they spend too many abilities, they're not gonna do so hot against the big guy himself! On the other hand, their next mission makes them sneak out and sabotauge enemy supply lines; something more skill based could be a lot of fun here.
In the end, the best thing about having the PCs in a big war scenario is that there are almost COUNTLESS numbers of fun - or evil

- things you can do with them. Almost any kind of encounter you want can be done here.