Wait, where are you copying to and from?
Generally, when you do a mod, you make it by doing the following:
Create a new folder in the My Documents/My Games/Sid Meier's Civilization 4/Mods folder.
Inside that folder, create a folder called Assets.
Now, whenever you need to change a file, you copy the file into the new Assets folder you've just created, adhering to the same directory structure of the original Civ4.. So, if you wanted to replace Civ4UnitInfos.xml, you'd make a new directory in this assets folder called "xml" (if you haven't created it yet), then make a new folder in that folder called "units" (if you haven't created that yet). Then you can copy the original version of the file into this new directory once, and modify it there. Take a look at the example mods that come with to see an example.
While it is true that you could very well copy all the files and folders in the asset folders into your mod project to begin, it's probably not a good idea, since later when you want to package it you'd be including files that are unchanged, which would just make your package larger. Any file that you don't include in your mod will automatically have the default file used.
Hope that helps!