I use this box to stack my RX above my CC3D ATOM. I used it on a PS-240 X-Quad ( http://www.thingiverse.com/thing:1429311 ).

Just mount it above the CC3D ATOM, fix your RX with a zip-tie and use two Zip-ties to fix your antenna on the left an right.

V2 is a bit lower, with thinner top, front wall and an opening for USB. Use V2 for CC3D Atom tight spaces, the original Version may fits also to other FCs.

Maybe you also like the complete stack for CC3D atom: http://www.thingiverse.com/thing:1684887