I'm just trying to find out where to place them after I have modified them in order for the game to use the modified file (and not replace it).
Answer

They're in folders in the main EB directory simply called "sp game edu backup" and "mp game edu backup".
Every time you start RTW vie trivial script data from mp or sp backup directory is copied over to Data directory.

So dont change files in Data directory but in those 2 backup folders.
Take note though that this folders also contain map.rwm files, so if you do changes that effects map.rwm file you should replace them with brand new map.rwm files generated for your modified EB.