Quick question, sorry would have searched if the function worked.

Will Blue Marble terrain (or any other mod that is to be installed in the 'My Documents\My Games..\CustomAssets\' location, such as the Gaia Mod) need to be merged with a mod (such as Realism, Lost Units, etc) to work? Or will Civ load what's in CustomAssets, then load the Mod on top, leaving both working?

I'd suggest merging them together, unless they share common elements. Then, you'll have to mod them together and hope that some elements don't overlap. If they do, you can use your own judgement on what you'd like.