Alright... since no one helped us, I looked into this some more, and found out what do do.
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1. Open GTK/JK2Radiant and goto your Project Settings (File, Project Settings)
2. Make sure it is set on Multiplayer mapping, and where it says fs_game, type in "hydroball" (Without quotes. If your hydroball directory is named something else, put that in instead.)
3. Quit Radiant.
4. In your hydroball folder, make a directory called scripts.
5. Download this file -
http://100megs9.com/~ishionu/other/hydroball.def - and put in in the scripts folder you just made.
6. Open Radiant, and marvel at the new entities in your list ;D
7. Build your level, compile, and play. It will be located in Gamedata/hydroball/maps (that is where the .map files will be saved, also)
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I hope this helps the people trying to make Hydroball maps.