Ahh, you found me... Run!
If i were to draw a overlord boss card but he is the overlord for the game which one do i fight? plus if he is a overlord but not one for the game i am playing can i still fight him and if so does the game end there or is he treated like another boss not overlord this game?
It is fortunately quite simple: as stated in the rules, if the Overlord for the main game is one in a dungeon, they replace the third level of that dungeon.
So if the snake-lady Vaash is the overlord, then when you beat the 2nd stage of Coilfang Resevoir, you go to her (ignoring the stage three deck) and will fight her next turn.