I have several Ally and Villain packs and I want the ability to easily add or remove all the cards related to the pack. I'm just wondering if people have found an easy way to mark these? I was thinking of buying some small colored sticker-dots to stick on all the cards in the same pack and then sleeve them. Has anyone found a better way to mark these, or am I the only one who seems to be concerned about this?

What's the purpose of removing cards unique to a single pack?

And how often would you need to do that, that it's easy enough to just cross-reference with a list or webpage giving the inventory of each pack?

if you ever wanted to sell a pack after mixing up all the cards just go to boardwars.eu to see their complete assets photo library

I don't want to load all my decks with all my packs.

When I start a campaign, I may only choose 4 different allies and 4 different villains. So I want the ease of swapping the cards out without having to look the list of cards on each rules sheet. Also, since I play with different groups, I need the ability to switch these out easily.

Maybe the most feasible way would to be to sort cards according to wave?

That being said, it shouldn't take long to figure out deployment cards, if that's what you're worried about. And Agenda sets are clearly labeled- you could always just create a document listing which Agenda set came with each wave.

Other than that- I don't see much point in separating all the cards (item cards, command cards, etc). I think you can probably mix those in fine.

Playing physically is not the same as PBF, but one alternative....

If you have a tablet or laptop that runs Java, you could handle the book-keeping of the separate campaigns using the Vassal campaign module. You would only need the physical cards during the mission as reference.