I did something similar, some time ago:
* Leave the smoke layer on top, and set it to "Luminosity" mode; no need to perform any selecting or masking.
* Create a new layer, below the smoke layer, and render some cloud-like random colors there.
* Adjust and tweak.
(PS: I did this using GIMP, not Photoshop; hope my translation from GIMP to Photoshop is accurate)