if you're getting a cover you'll definitely want a roof system.. the overhead racks from nissan won't work so well with a cover, it'd have to be custom. if you are getting a hard cover some company's manufacture ladder racks that will go on the outside of the cover and bolt to the bed... that is also an option. I guess it all depends on the look you wish to achieve.. I have the OEM overhead racks and my buddies call me 'carpenter' when they are on... whatever, Titan envy.
There is also a thread on here where some one used the armada roof rack on their titan, looked sharp!