I just starting playing with Shadowed UF. Shadowed is what it is: A light resource unit frame addon. It is not suppose to have a large amount of functionality. It's lightness is it's attractiveness.
That being said, I do not know if runes can be moved but it would not surprise me if they could not.
One solution though is to just get a rune mod to use. I personally use a round-about way via IceHud. I use the hud for things other than health and mana. (Only runes, Combo Points, SnD, Runic power, Shadow Infusion, etc...) all with custom settings). But I am trying to change that anyways.