The default shortcuts used to start EB1.1 use the "trivial script", which is installed during the installation of EB. Basically the script makes things easier for common players but a bit harder for modders

Whenever you start the game with the trivial script, it backups some of your files (including the EDU) with other files contained in "...\EB\mp game edu backup" or "...\EB\sp game edu backup", depending if you are starting the game as single player or multiplayer.
Thus, if you want to change your EDUs, you have to change the ones contained within those two folders.

Specifically, to play custom battles, you need to change the EDU contained in the "...\EB\mp game edu backup" folder and then start the game as "multiplayer" using the trivial script. Starting it as single player works as well, but some units will be missing.