A: 

This is because the two different files represent the same layout just in different configurations. If you want to edit the landscape layout you have to click on the 'Layout' tab at the bottom of the editor and select the 'Config' that you want to edit. Depending on the configuration you select you'll have the layout xml editor fill with the correct contents from each file.

Qberticus
Ah, I see. Thanks for the clarification.
wirbly
A: 

Right click on main.mxl and choose 'new editor'- this will create another main.xml which you can replace with the landscape version via a double click.

However, eclipse does this for a reason- so you don't get confused and bork your files up.

I would think you also could edit these files in a text editor to the side with little loss of efficiency.

Mischa
My method lets you open both at once, also putting a comment near the top such as <!-- portrait mode --> helps avoid confusion of which file is open.
Mischa
I actually don't see a "new editor" open when I right click any of the layout files. Am I missing it?
wirbly
Sorry! I wasn't entirely clear- first open main.xml, then on it's title above the text editor area is where you should be able to right-click. After choosing a new editor, you will have that file open twice, and can double-click the landscape version to have both open. Very handy to cut and paste between the files, just be sure to comment the code so you never get 'lost'!
Mischa
Ah, I see now. Great tip - thanks!
wirbly