Tom Guilmette has created this nice video walkthrough of Phantom HD Gold operation with the on-camera controls. Usually when I use the camera, I'm at my cart tethered to it with the laptop because it's less intrusive on the camera department for me to interface remotely. Sometimes though this is impractical and you've got to get your hands on it. I've found usually if I'm having problems with the black reference when interfacing remotely, doing it from the side of the camera instead will fix the issue. That's the thing about the Phantom, it's a little buggy no matter how you work with it and at some point, I'd like to create a list of consistent problems I've identified and their work throughs. Save that for another day.
He also has this useful blog post accompanying the video available here:
It's content like this that's most valuable to video users of all skill levels the world over. Once you've landed your first Phantom gig, it's nice that now there's a great resource available to walk you through its basic operation. I wish something like this had been available when I did my first shoot.