To make OBS to follow the active app window, Tools->Automatic Scene Switcher exists. It watches the window title of the active app and automatically activates the scene that is associated with a given window title.
To make the Automatic Scene Switcher work, it's necessary all windows you intend to switch to have distinct window titles. I don't know World of Warcraft, but usually such games simply show one and the same title, so additional work is required. You need to use a window title changer to give both WoW instances distinct window titles if they don't already have it.
Autohotkey can be used for setting window titles, but I don't have any example. You will probably find many google search hits for this task.