I found this in the FAQ:

Q: In custom battles or multiplayer the unit selection is missing units.
A: All of the regionals cause a problem for the custom battle / multiplayer list. There is a special EDU for custom battles / multiplayer in the "...Rome- Total War\EB\mp custom game edu" folder. Rename your campaign EDU then place the EDU from that folder into the "...Rome - Total War\EB\Data" folder. When you want to play a campaign again, switch back to your original EDU. EB v1.1 now comes with the trivial script, which will automatically switch the files for you. To play custom battles or multiplayer battles with all of your factional units, run the "Play Multiplayer" option of the trivial script.

Apparently the Trivial Script (optional installation item) is what switches the files for you, and you have to switch them back when you want to play a campaign. Never tried it myself as I don't play custom battles.