I don't know if you just can't do this, but whenever I do Skirmish Mode in Cortex Command, I make a base that I think is pretty cool. I hold down right-click and move the mouse over the save scene option, but it's crossed out and I can't click it. Is this a common problem or is my copy messed up?

That's probably detritus from scene editor mode. You can't save bases in skirmish mode.

Oh, I see. Thanks! Wait, can you use mods in the scene editor?

Yes and no. The surefire way to make sure the mods that you want to load are loaded is to move their index.ini type declarations (includefile) to base.rte/index.ini, but I believe that you can use any mods in a .rte that you create the scene in. I may be wrong, I've never tried it myself.
Either case, mods do not usually load by themselves into the scene editor. You have to do special things.

"special things" here meaning choose the .rte you want to create the scene in as whatevermodyouwanttoinclude.rte when creating a new scene.

So I go to Base.rte/Index.ini and type (if i want to use the invincible blocks) IncludeFile = Xtremeblock.rte/XtremeBlock.ini?

EDIT: Oh crap. Nevermind. That crashed my Cortex Command and now I can't seem to move the original Index.ini back. Help!