Bukkit

• Download IslandWorld.jar and copy into your plugin folder.
• Install CleanroomGenerator or other plugin to generate empty world.
• Start server and wait until is fully loaded and islandworld create default config on disc

With multiverse plugin

• Create empty world:

  /mvcreate IslandWorld NORMAL -g CleanroomGenerator:.
  

• If you want other world like water world you need to add block and height into params:

  /mvcreate IslandWorld NORMAL -g CleanroomGenerator:100,water
  

• Make sure that height (in that example 100) is identical with island-height config option!
• Stop server
• Make sure that your worlds in IslandWorld config (world-isle and world-spawn) are correct !
• Adjust other config options
• Start server

Without multiverse plugin

• Stop server
• Add into bukkit.yml on end:

worlds:
  IslandWorld:
    generator: CleanroomGenerator:.

• Make sure that your worlds in IslandWorld config (world-isle and world-spawn) level-name from server.properties and world in bukkit.yml are identical !
• Adjust other config options
• If you have already world generated on disc delete whole world folder it will be generated again on server start with correct generator
• Start server