This app was mentioned in 9 comments, with an average of 1.89 upvotes
There is an app on android by Cool Grass; I'm not sure if it's also on iOS. Here is the android version if you have access to that:
https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log
There's actually a really neat <em>Android</em> app for campaign tracking. There's also the campaign log on the back of the Campaign guide, where you can write on it, or make a copy of it, to keep track of what you've played and where you go next.
The side missions, once selected are shuffled and kept in a separate pile, it's a really easy process and it's really just one more thing to keep track of in a multi-session game, not too crazy. I would recommend adding any expansions to the side mission deck first, so you're not fiddling with it during your campaign.
Edit - Added app specifics and a link
There is an app for Android, called Campaign Tracker for Imperial Assault that is pretty awesome.
It tracks the missions (including the rewards after you select who won), all the upgrade cards, agenda decks and rewards.
You can get it at the following link https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log
I don't know if there's an alternative on iOS, but maybe anyone at your group has an android device you all can use, since there is no hidden info on the app so anyone can track it.
To answer your first question, here is the app I've been using since I'm running two separate games: https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log&hl=en I've really enjoyed it. It tracks experience, money, items, even things like agenda decks. It's unofficial, and it isn't pretty, but it's free.
I generally run it more GM style, and thus the rebels win far more often, but every once in a while I play hard and win one just to keep up the sense of danger. That said, the core campaign tends to skew towards the rebels in my opinion anyways, so you can play pretty competitively without worrying too much about them losing all the time.
The side campaigns work best as their own thing I believe, but the characters and items can be used in any playthrough.
They mostly add characters and side missions, but that doesn't mean they're not worthwhile. I really like the new characters, and the Bespin missions really add some variety to the game (I own all the boxed expansions, but haven't run any of the Twin Suns stuff yet). That said, don't underestimate the value of the skirmish game. I bought IA thinking I'd never use it, but it's rapidly becoming my preferred way to play.
That's a rough question, personally I think Bespin gave me the best bang for my buck, but as I said earlier, I haven't played any Twin Suns missions yet, and I just got Jabba's Realm, so I'm no authority here.
Hey, good job on this! Theres an app for it on android that does pretty much all that, for those who want it. Me and my partner use it, as well as our game group
https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log
Yeah I can recommend this one too https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log
Sucks that you can't transfer the save state to a different phone though.
https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log is the one I'm using.
https://play.google.com/store/apps/details?id=com.gau.ia.campaign.log&hl=en
This is the one I'm using. It's an Android app.