ummm, how? When I hit the green button for full screen, it takes over the screen like a Spaces screen. How are you able to have side by side full screen of 2 apps. That seems like you are breaking the definition of the word full. If 2 apps are "full" screen side by side, you either have "half" screen views or 2 monitors.
Open Mission Control and drag a window into an already full screen application. You can also drag two windows in a new full screen space, or drag a full screen space into another to merge them.
