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Chris, your guide scope needs to be rigidly fixed to the imaging scope so that it sees the same movement as the main scope.
Basically, you need to wire up:
1) the mount to the computer
2) the guide cam to the computer
3) (optionally) the camera to the computer
As described above, PHD will lock onto a star that the guide cam sees. The guide cam takes an image regularly. If the star moves in the crosshairs, PHD will tell the mount to move to counter it until it's back in the centre. Rinse and repeat.
You don't have to use software to control the imaging camera, with a DSLR you can get away with an intervalometer. But it's nice to see the images roll in one by one.
With an EQ6, you'll want to use EQMOD and ASCOM to be able to control the mount and present a controllable interface to other software. PHD will connect to ASCOM to send it push commands. Image capture software often includes functions to slew the mount, plate solve, dither, etc.
Dithering is a process where after every x amount of frames, the mount is moved a few pixels in a random direction. This shifts the object in the image slightly, but since the hot pixels are in fixed positions on the sensor and not with respect to the FOV, they get eliminated during stacking since only "real" signal is retained.
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