The command chair is where the marine's commander will sit to be the commander. It is the equivalent of the alien's hive.
They can only be built on specific locations on the map. Unlike the hive for the alien, having several command chair is only useful for having a backup a command station in case of the destruction of the main command chair.
You can see if a command chair is available mainly by looking on the left side of your screen, under your map, when the inscription in big red letter "NO COMMANDER" appear, or when you walk by an open command chair, the screen says "LOG IN" (if no one is commanding) or "LOCKED" when someone is.