Yeah you got it. In the final project there is probably going to be 4 layers. Layer 1 for backgrounds, layer 2 for tiles and characters, layer 3 for menus and buttons and layer 4 for mouse and other things that need to always be on top.
As for the scaling of images on mobile devices that is good to know. I was plaining to work on a mobile game next year and I'll keep that in mind.
I'll make a video explaining the roatation and z ordering next week if I get the time.
Also about the actors using images. You can maybe have 10 huge acotrs on screen before a gmae starts spazzing out if you use the native animations in Stencyl. With this system you can have 100 without a problem. This is all on exe games not sure about flash.