for CC3D you need dRonin "Artifice" Release-20170213.1 -- support for CC3D was dropped in newer releases.
get the dRonin bootloader flashed onto the CC3D the same way you did LibrePilot.. you can use either LibrePilot GCS or dRonin GCS to flash the dRonin CC3D bootloader bin
file.
after that dRonin GCS can be used to flash the "Artifice" fw onto the FC.