CWR supports custom generation. This should work with most generators (tested on Terra and Iris).
WARNING: Make sure to add the generator under the world in bukkit.yml or weird chunk glitches can occur! (Properly reboot the server afterward setting it)
Example using Terra (Bukkit.yml):
Setting the generator
Once it has been added, you can now add to CWR using: /cwr edit <world> setGenerator Terra:DEFAULT (replace Terra:DEFAULT with your generator name. Please review the custom generator's plugin instructions for how to do so). During the next reset, it will use this generator.
NOTE: If the generator is already under the world in bukkit.yml and the world is already loaded (using that generator), you can set the generator as DEFAULT in CWR. It will continue using this generator.