I've answered this question earlier somewhere, but cba to find the actual topic, so I'll just explain it again.(We should get a sticky for custom race companion creating tbh.)
In order to create a custom race companion with CM Partners, you need to open up the CM Partner files and the custom race.esp. Once you've opened them up, open the character->race menu and right click on the custom race, choose duplicate, you will need to do the same with eyes and hairstyles. Once you're done creating the duplicates, keep all the tabs open and open 'body data' tab in the duplicated race and drag & drop the hairstyles to the 'hair styles' window and eyes to the 'eyes' window. After you're done with this make the duplicated race unplayable, so it will be NPC only, rename the duplicated race to something else than the original from which it was duplicated from to avoid confusion when you're choosing the race of the NPC, click ok on all the tabs to close and save the changes. Now you can use the race, eyes & hair of the custom race on the duplicated one on an NPC without it resetting the face, eyes & hair to a blind, bald, vampire. Once you're done with this, save the .esp and reload it again without the custom race .esp, only the CM mods active, give it the finishing touches and save again. If you intend to publish the mod, remember to put the race mod you're using in the requirements and if possible, give a link to the file also. Credits etc. should be pretty clear.