I just put mine in yesterday and as they said, you set up the spacer based on the thickness of your glass, attach the strain relief on the dry side so that if it falls it doesn't break anything, make small adjustments with it running on full power to line up the wet and dry sides and then throttle it back the way you like it and pick the mode by pressing the black mode button and cycling through the various modes. I have mine set on lagoon. It's amazing how much thrust it has on full power. You should also do the calibration to allow it to shut down should it fall off. The instructions are in the manual.
I've had a separate thread asking if anyone has tried hooking up a gel cell to the 12v input and am still waiting to find the first adventurous soul...