Are you talking about in the unit frames or in the HUD?
You can move them by editing either [ Interface > AddOns > nUI > Layouts > Default > HUDLayouts > {hud mode} > nUI_HUDSkin_{hud mode}_Player.lua ] or editing [ Interface > AddOns > nUI > Layouts > Default > UnitPanels > {panel mode} > nUI_UnitSkin_{panel mode}_Player.lua ] -- In either case, look for the ["Runes"] section and modify yOfs to move the runes up or down or modify xOfs to move them left or right.
Keep in mind that moving the runes "just a tad lower" than they are in the HUD will likely cause them to overlap your HOT/DOT bar.
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