The normal, official Battlegrounds scripts come enabled, so you don't need to make any changes. They're located in npc/battleground/. There are different types of matches, which you can read about on iRO Wiki.
The "custom" battlegrounds have been moved into npc/custom/battleground/unofficial/ as of 163a98c to avoid confusion. As stated in npc/scripts_custom.conf, they are custom implementations of the official scripts which were written before the Aegis conversion (i.e. the accurate, official scripts currently in npc/battleground/). As such, they shouldn't be used, and are still there largely for history; however, if you prefer them to the official scripts, comment out the official scripts and uncomment the custom ones (since they have identical names).