Supreme Commander

Supreme Commander is a high Covenant rank. For most of the Covenant's history, this rank was held solely by the Elite race, but was gradually mixed then replaced completely by Brutes after the Great Schism. They command fleets, and armadas.

Rank
The Supreme commander is indeed placed in the position of a high rank generally organized within the sophisticated and complex Covenant. It is certain to say that this particular commander has the rightful purpose of commandeering a fleet of a possibly unknown amount of the Covenant's well-built and advanced warships. It would be unjust to say that the Supreme Commander is below the Imperial Admiral or repeating over to a conclusion referring to the fact that the Supreme Commander is above the Imperial Admiral. It may be possible that Imperial Admiral isn't really of the Covenant but is more of a Heretic and rebellion rank but this is also just speculation. For now it is that we must see and play the "which-is-which" game or simply wait until solid proof is released possibly in future novels, graphical novels/comics, or maybe even Halo 3. However, it is in fact quite interestingly possible that the Supreme Commander is below the deadly yet clever and precise Councilor along with the well honored Arbiter (Saying that it is below the Arbiter opposes and challenges against the fact that Arbiter may not really play a military role of commanding others which also goes along the Sangheili Councilors).

Physical Appearance
When commanding a fleet, Supreme Commanders wear violet armor with a cloak that wraps around and over the armor piece of their shoulders. However, when the Arbiter was being tried for the destruction of Halo, he wore golden Zealot armor, which could signify that Supreme Commander is one of several Zealot ranks, although this has yet to be confirmed. The fact that the Arbiter wore the golden armor of a Zealot yet wore an unknown violet pigmented armor is quite odd. It could also prove that the creators/creator of that particular story part were exaggerating the Supreme Commander's appearance to allow the story to become a bit more interesting. To prove this theory generally in Sunrise Over New Mombassa the elites and there weapons appear to be exaggerated also. Ex. The plasma swords are pink along with the fact that plasma rifles shoot green beams opposing to the fact that the original plasma rifles seen shoot cyan repeater-type bolts.

Halo Graphic Novel
The particular Supreme Commander in the aforementioned text was a friend of and yet superior to Rtas 'Vadumee, and would later become the Arbiter. During the Civil War of the Covenant, it is possible the Brutes usurped these positions from the Elites. But even so some Supreme Commanders escaped to fight the Brutes.