Put the sovereign rune in the altar with 1 draconic rune (or whatever the smallest runes are that you turn in for your armor).
It will crunch it into 1-3 eldritch runes, 1 tempest rune or 1 sovereign rune in order of likelihood.
Put 3 eldritch runes into the eldritch altar and you'll get 1 random tempest run
3 tempest into the tempest altar you'll get 1 random sovereign rune