The cells are used in order. Heroines can be shuffled around by reseting and upgradeing devices, but villains stay in the first cell they get. So if you start a new game, you can do a bit of planning.
You can wait until you have Audrey, Galatea and Chesire. Then you can put 3 heroines in cells "as a placeholder" to fill the first collumn. Then you can put in cells whoever you want to fill the rest. Lastly you reset the devices of the 3 placeholder girls to free the space for Blackfire, Superwoman and Killer Frost. It is tedious and costly, but at least you can cheat to get the money.