you need to use the admin from WEBi, add all the CMOD server you want, and then assign it to your desktop.
Or modify directly the xml files in the config directory from WEBi installation.
Stop and restart WEBi, and that should be it...
Am I missing something in your needs? Because it is really simple... no need to create a new desktop for each CMOD server... you can, but not necessary.
Sincerely yours,
Alessandro