I store my decks just like dennis. Even if I didn't though, the color of the text on the bases matches the color of the text on its faction.
I place them with the associated faction because it makes it more thematic that way and removes the possibility of getting Cthulhu or Munchkin nonsense unless you absolutely want it.
I kinda like doing it by expansion because some factions have bases where other factions absolutely kill it. Like robots on at the zombie mall, innsmouth in the alien world, or any faction that can move other peoples minions (pirates bears and tornados) and the ninja bases.