tunepunk,
I realized I never really answered your question above -- sorry!
Trying to make a 3D game with a 2D layout editor is a pain in the neck. For Robot Rumble I made the mistake of laying everything out in a side view rather than a top-down view. This meant that I had to do a lot of trial and error to figure out how everything would look when my camera was top-down.
In the tutorial I intentionally did a top-down layout for the top-down camera. This way it is a lot easier to manually place items. I recommend setting the (x,y) position and the (x width,y width) size in the editor, then creating an in-game camera that you can move around, and tweaking the z-size and z-position of the objects according to what looks right.
TL:DR
For a top-down game, use a top-down layout in the C2 editor.
For a side-scrolling game, use a side view layout in the C2 editor.
For a 1st-person or 3rd-person game, use a top-down layout in the C2 editor.