Guitar tuning problems.?

My new B.C. Rich - Kerry King V just arrived. It has a Kahler Bridge and locking nuts. And it just wont seem to go into tune, this is my first guitar with a kahler and tremolo, and Im not really familiar with how to work it. Can someone please tell me how to tune it properly? I have been using a tuner. When I try and tune the Low E to D# it comes up that its tuned to D# But it doesn't sound right at all. This may sound really nooby, but I am a noob at guitar unfortunately. :/ Thanks.