David:
There have been other threads on this subject. You can search the site. I have done a bit of shooting from boats in my quest for loons.
One of my goals was to get as low as I could, and also be able to keep the camera ready for long periods of time ( sometimes several hours if light holds) as I wait for wing flaps and interesting behaviour. You might want to look at my camera mount.
http://www.birdphotographers.net/for...ad.php?t=44629
This is mounted in my 16 ft. Lund, adjustable for height. I sit in the bottom of the boat to reduce my profile and reduce stress on the birds. I control the boat with a foot pedal for the trolling motor. Usually have even the trolling motor off when shooting.
If the birds are flying, i will shoot handheld, but since loons rarely fly, that is less of a concern. I usually have two bodies out, one with the 500 on the pedestal, and the other with a 70-300 zoom sitting at my side for quick grab shots. Occ. the loons come in so close I can't depress my 500 enough to clear the gunwale, and will use the handheld rig. Also for when they dive under the boat and I am shooting them underwater.
There are many folks on the site that do excellent work on flying birds from boats, handheld, but my needs are served well by the above setup.
Good luck.
Randy