"Command" Master Chief is just a title. The chief's rank is master chief petty officer, and his position aboard the command/ship/etc. is the senior enlisted advisor to the CO. So, if a senior chief petty officer holds the position of senior enlisted advisor, he is called the Command Senior Chief.
Unlike the army and air force, the Navy doesn't provide different rank names for their senior enlisted advisors; this stems from the naval tradition of commanders not needing to look over a battlefield and tell which troops belong to him. Therefore, the naval service never required the more distinct uniforms that the army uses in their working environment.
So, to turn this into a Starfleet answer, the senior enlisted advisor should be the highest-ranking enlisted character on the ship. If it's a senior chief, then calling him the Command Senior Chief is entirely appropriate. Note that Starfleet may differ from the U.S. Navy in that the position may be a collateral duty (rather than the chief's only job, as it is at most commands in the Navy). So, the chief will likely also be the Senior Chief Warp Drive Technician in addition to being the Command Senior Chief.
For a Chief as the senior enlisted advisor, I would suggest using the submarine title "Chief of the Boat" (which applies to the senior-most enlisted crewmember aboard the sub of chief petty officer rank or higher...I don't know off-hand if subs carry a separate senior enlisted advisor, due to crew size constraints).
If, for some reason, your ship is so small that the highest-ranking enlist is of petty officer rank, then I would suggest using the title "Leading Petty Officer" (which is generally used for the highest-ranking petty officer in a division when there is no chief between him and the division officer).
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz