Custom libraries don't overwrite anything, as long as the file name is different from default libraries. If the date of the custom library is newer than the date of the default libraries, objects in the custom library will take precedence over the default objects and replace them
in game.
You can use the Touch program (
http://farc.3synergy.net/misc/Touchexe.zip) to make sure the file date of custom libraries you use are newer than your Fighters Anthology default libraries (which will have the file date when you installed the game).
Hope this helps,
Zephyr