Ok, I've been looking through the manual and browsing the forums but I'm still confused as to the purpose of putting an object in the scene.
My general issue with it is that at the start of the game, it messes with the player character right away despite setting it outside of the layer space (with destroy outside of layer turned on).
What I want to know is the proper etiquette to getting the object to work (it's suppose to be spawning an instance of the object on mouse click) when the spawn event occurs only.
You should destroy all objects at the start of the game, that are supposed to be spawned during the game to avoid problem.
And use another object or system to spawn them at runtime.
This post might be helpful.
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You can also make a layout for objects only, it never shows in the game, but it can hold all your sprites. The objects don't have to appear on all the layouts, just one of them.
Thanks, that actually explains a lot about the structure.