I'm not exactly sure what you're asking. The M13 is technically always in a scene, but how you're looking at the scene and how the M13 behaves when you go from one scene to another can be changed.
If you're in latch scene mode, when you choose to activate a scene, the list of 12 scenes remains on the LCDs. This enables to immediately go to any of those scene by pressing the corresponding footswitch for the scene you wish to make active. To go into a scene to edit it or turn individual effects on and off, you hit the "scenes" switch.
If you're in momentary scene mode, the default state is kind of inside a scene. To go to the scene selection view, you hit "scenes" switch, select the scene you wish to go to, and then the M13 will be in that scene. You'll be able to edit and turn individual effects on and off immediately.
Does that relate at all to your question?