Do full conversion mods overwrite the original Civ 3 game files? If it does, can you play it as a scenario and not as a full conversion mod? Also, can you make another copy of Civ 3 in a separate folder so you can play a mod and the game?

"Full conversion" just means that the game was completely redesigned from the ground up, instead of built as a set of changes to the original. There is no difference in the way the files are used, though "full conversion" mods generally include much more artwork that will seem to have "replaced" the originals in-game. All mods should be confined to a folder in the Scenarios directory, and not overwrite any of the original files.

edit: This may not be true of vanilla Civ3, which did not use the mod folder system.