It will depend on the version you are running, you'll have to read the docs on their www site. All the knobs are for different rpm ranges or purposes, but the best bet is to just set the BASE knob according to what injectors you have in, and then use an afc to fine tune it. Each click to the right (clockwise) is -5%.
example: I have 650cc injectors installed, which are roughly 30% bigger than the stock 450's, so I have mine set six clicks to the right. I shut it up, and then tuned normally with the afc. Otherwise, just leave everything set to zero and tune with the afc, that'll work too (I've done both).
http://www.fullthrottletech.com/forumdisplay.php?f=40
As for water inside the box, yea, that can be an issue. I'm not sure why the unit is not equiped with some sort of rubber seal around the lip of the cover. I put a very thin bead of rtv around the lip on the cover & let it dry. Then when you screw it back down it will have a nice seal to prevent the water intrusion problem.
Good luck.