In D&D, experience is tied to a character. You take a character through a challenge, if "he" succeeds, that character gets experience. This does not need to be true, and it's actually kind of counterintuitive. Experience and advancement are metagame things, they reward the player, not the character. Characters get in-game rewards like status and wealth and nifty loot.
In TSR's old game system, Amazing Engine, experience points were awarded to the player, who could distribute them for advancement among his pool of characters, whether those characters were in the same universe or not (completing a scenario in Bug Hunt could give you experience you might use on a character for a Once and Future King game). This was a blatent attempt by TSR to cross-promote these games, so people would "Gotta collect them all!", but it was also a neat idea, especially for multi-character play.
The easiest way to do this would be to say that for your game, players have two characters, each of which has the same experience as the other. That way they're interchangable, the players can swap them in and out as necessary without worrying that one is falling behind. Keep track of the xp points by player, not character. They reward the player for showing up and playing well.