Panoramas are your first and second layer, pictures are your overhang. It's really no more complicated than that.
After you've set your panorama, you'll have to manually put in blank (or not, I guess it depends on your map) "Same Layer as Hero" events to keep players off of the ground they're not supposed to be on.
The pictures are more or less self explanatory. The highest number is always displayed on top when two or more pictures occupy the same space. There is a built in limit in rm2k/3, 40 pictures by default on a screen at a time, 120 with Aten's David/Goliath patch, so keep that in mind. You need to turn on the "Picture Scrolls With Map" option for your pictures to stay in place while your hero moves.
You CAN use pictures and panoramas that are bigger than what rm2k/3 will let you import by putting them directly into the respective resource folder. Doing this though, you will not be able to select a transparent color for your pictures (you never get that option anyway with panoramas).
Not quite sure what else I can explain, what you're asking is pretty straight forward.