Yes I'm doing every area as a seperate layout. This is so I can make add new areas really quick and have the player go to a random area each time he leaves one.
Just a quick thought, but what if you put them all in one layout separated by some space between them. Then, you could put a trigger at the end of each area that teleports the player and the camera to new coordinates which will be where the next area starts.
It'd load faster than going to a new layout (of course with maybe a longer set up time in programming). I couldn't say how well it would work without testing it, but maybe set up a function (or use "choose" or something) to choose the coordinates for the next area randomly (from a list of each area's starting coordinates). It would probably also require events or enemies to appear/activate once you enter each new section. You may also need to set up blocks so you can't move or pan the camera past the borders of each area.
Like I said, I couldn't say how well it would work without testing. I just thought I'd throw it out there.