Hasta La Motion!

for compositing purposes, I created a bunch of cloud clusters in my Maya scene and I rendered out the clouds separately.

but there is a big problem that I don’t know how to fix.
the rendered clouds are just black and white and with alpha of course, and after composite they can’t retain their original color and look .

please look at the pictures.
how I can manage to render the render layers to gain the original look ( which everything is in a single render pass)?

please help me with this
thank you in advance