The clouds are connected to the “SkyAtmosphere”. You can set the “Transform Mode” of the “SkyAtmosphere” to be not at the world origin and move the “SkyAtmosphere” down a few kilometers. So you world origin is in the sky where your level is and the clouds will be below.
The disk of a normal tropical cyclones is at an altitude of 17km. The sky starts to be black instead of blue at that altitude, so you probably shouldn’t go much higher than that with your sky Island. You can make the “Atmosphere Height” larger than the default 60km if you want the be very far up in the sky and still have a blue sky.