Each player is technically an agency, or some form of team, this is decided by the player and forms the backbone of their character. This agency has a roster of heroes they can call on to play the game with.
More than one player can have a hero in their roster, although only one player can use that hero in any one session. Players can either decide between themselves, it can be decided on a roll, or on a first come first serve basis.
During the game, players use the heroes to earn karma for their agency as well as for the individual hero being played, be it character created or a Marvel hero. Agency karma is then spent to build bases, recruit new heroes, or even create their own heroes.
Each Marvel hero used still develops its own pool of growing karma which is used for that hero to upgrade its abilities. Hero karma is spent by the GM to advance the heroes as they see fit, character created heros karma is spent by the player as they see fit.