I had the same issue with Monk "Chi" indicators and Paladin Holy Power meters.
You SHOULD (!) be able to adjust this via the Mover functions.
Invoke the System menu, go into the Interface settings, select Addons and then nUI, click the plus sign to expand the list of interface options, then on the General option, turn Movers ON.
This will turn most of your screen pink (thank you very much, pet battles overlay.)
Move the Pet Battles overlay DOWN until you can see a little pink rectangle in the midst of your screen. Check the name to make sure it's your DK Runes meter, then drag it to where you want it. Move the Pet Overlay back to where it was. Hit ESC to get your System menu back, go into Interface again, then navigate to Movers and toggle them OFF.
Test it out.
