EB mini-mods are all installed into the EB folder. How it works is, running EB doesn't even touch anything in the old RTW game, it just uses the RTW executable to open the files in it's own folder. Thus, a stand-alone mod.

You should uninstall it using the EB uninstaller, and take a look afterwards to check that the folder is definitely gone. Uninstaller should delete those EB-icons, and even if there are some left, they wouldn't affect a different mod.