You will have to use the software, for the manufacturer, of your motherboard, to control whatever you hook up to the motherboard header.
You can run other software, for like say a graphics card, as those typically require you to use their software, to control the RGB. Say you have a Zotac graphics card, you would have to use their software to control the RGB on it.
Now if the card and board manufacturer are the same, then the motherboard software can be used. Examples would be Asus graphics cards, and Asus motherboards that use Aura Sync, or Gigabyte cards and boards, that use RGB fusion 2.0.