So I'm in the middle of running the campaign and have been feeling lost now and then. Particularly with how to detail the various days in the war. I left off at day 3 so I still have time to figure it out. Has anyone ran this and have some advice for war running?

Egh. It really relies on the GM having an encyclopedic knowledge of what's meant to happen, and the imagination to make it all up when the players do something that the writers seem to have blithely assumed they would never do, staying on the rails. It's fun, and I've used the siege situation more than once since, with the players either being the defending or attacking force (At one point on a near-sector scale!) but I really found it to be quite painful. The army rules slow things down a lot unless you've got it down pat.