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Are you using the nUI6 alpha? If you are, then it does not have the runes yet. If you're not a use familiar with nUI then I would not recommend using the nUI6 alpha version. Stick with nUI5.
That said, the DK runes are shown both on your unit frame and in the HUD. I *strongly* recommend using the HUD... there's a red button at the top center of the display you can click to change HUD modes... the usual selection is "Player/Target"
As for customizing the layout, nUI5 is fully customizable, but you have to hand edit the layout files in [ World of Warcraft > Interface > AddOns > nUI > Layouts > Default ] to do that. nUI6+ will add a GUI tool for doing that.
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