The overlap is caused by the cooldown aura bar getting too big and wrapping. What class are you playing? You might try using '/nui hud cdmin 10' and see if that fixes that problem for you.
As for Omen and Recount -- you need to download either the "Stats" or "Dual Stats" plugin from the "nUI: Info Panel Plugins" section at
http://files.nUIaddon.com -- As an alternative to using Omen3, Recount and the plugin, you could install Skada instead which does the task of all three in a single mod.