When you generate your script, a separate file will be created containing the command codes and parameters for those commands. You just load this file back into the editor, and you can begin working again.
You can save as only a Script Data File if you wish, but I will always force a Script Data File to be generated with a Script File in case their were mistakes made.
As for the Visual Aspect, yes, you get to see what you are doing. Coordinates are plotted for you, so you don't have to think about position or use much math to figure where things should go. You just place it. Easy.
As for layers, I am experimenting with a few ways of rendering multilayer canvases, and it will depend on how many I can get working correctly. Right now, a good estimate would be Three (Background, Window, and Data). For the Battle Editor, I may have four layers (Background, Battler, Window, and Data). All of these are listed from Furthest Back to Closets Up.
Peace.