Yes it runs for all games in the PT - the one you have running and the other slots in that game.
I have 3 game slots in my PT and they are all runing at the water level I set for 1 game!!
If you have the _bug_ collector running it will remmebr which game you are in - DO NOT RESET it for eaach game as you will lose the settings and have to reset it all over again!!!!!!