@l33twash0r: a quick solution is to create several projects, with everyone of them containing only one part of the whole game. You then export them in different folders. By using the CallJS plugin, or Browser plugin, you then set some rules to go to another URL when a condition is met (leaving a world, passing a door...). Of course, that new URL is the one going to another exported part of your game.
You perhaps need to change the logo.png in each of those directories with a picture or something explaining to the user he isn't leaving the game, just going in another part of it.