You typically want to position the submersed unit as deep as possible around the structure you wish to protect; this allows the warmer waters to be pushed towards the surface and the thrust to keep ice from forming.
If the depth around your dock is very deep then you don't want to place your bubbler too deep. A maximum depth would probably be around 15 feet. Most of the dock mount kits allow for a 10 foot pole so if you can put the unit at a 10 foot depth you will be fine.
If you are in a shallow area then you should try and position the unit as deep as possible but allow 18 inches off the bottom.
As a rule of thumb, for every foot of submergence, a deicer will keep an area of around 7' - 9' in diameter. Windchill, air temperature and sunlight can significantly change this formula so use it as an estimator only. The angle which the deicer is suspended will also change the size and shape of the ice free zone.
There is more information here: http://www.thepondreport.com/dock-bubbler-deicer.shtml