Each layout is a level for the most part. Or each layout can be a part of a level. Anything that needs to be persisted between layouts should be tracked with global variables. It is advised to have one layout that has a copy of all your sprites (one that the player never actually goes to) so that you can spawn instances of sprites without any errors. You cannot spawn an instance of a sprite if it does not exist in at least one layout. So create a sandbox layout, put one copy of each sprite in it and then just never let the player go to that particular layout. You can then use events to spawn instances of any of your sprites in any of your other layouts without issues.
The manual and basic tutorials cover all of this in pretty good detail so I definitely recommend going through them. Hope this helps.