Are you asking "Is it better to install EB in the original RTW installation folder or in the copied folder?"

In that case, it's the same; installing in a copied folder is better so you have a backup of your vanilla installation (if you mess up too much with EB, you can always recopy everything and reinstall EB only, without installing RTW again)

Also, some mods are not completely including in their own mod folder and change some of the original vanilla files. If you install them in the same folder as EB, thay might conflict.