This app was mentioned in 3 comments, with an average of 1.67 upvotes
I've always stored my command cards separately than the deployments, mostly because I play campaign more than skirmish.
I keep my command cards in a notebook with small card sleeve sheets and they're organized somewhat. So I have one page per faction, for example, then keep all the other restricted cards grouped together, then the rest of them sorted by point value.
Like /u/fireresistant said, when list building you'll usually pick your deployment cards first then build your command deck around it.
I really like the Startactics app for this: https://play.google.com/store/apps/details?id=com.shinayser.imperialassaultmanager
For the list builder section I'd definitely add the app Startactics. https://play.google.com/store/apps/details?id=com.shinayser.imperialassaultmanager&hl=en
My list builder:
https://play.google.com/store/apps/details?id=com.shinayser.imperialassaultmanager
Podcasts:
Board Wars, Vader's Finest, New Orders