We are trying to complete installation of electric fencing, but it seems the previous owners built a deck over where I suspect the grounding rod is. The location of the charger box is off the deteched garage away from the meter box on main house. Is there a way to ground the charger other than planting a ground rod in our rock infested soil?

An electric fence charger must have it's own grounding system.

Here is a guide to the how and some of the whys that go with them.
Electric Fence - How To Install (http://www.afence.com/Electric_Fence/how_to_elecfence/elecinstall.htm)

There really is no good way to make it work well without good ground rod(s). Your electric fence will only be as good as it's ground. If you are in a wet location it is fairly easy to get a good ground, but dryer soil requires several ground rods (space them 6-8 ft apart and electrically bond them together WELL) to get good operation. And don't use a cheesy little wire for the ground conductor.

I have used solar powered electric fences for many years, and besides weeds on the fence, my worst problems were bad grounds. Once I learned that, life was better. Now I live in town and don't need that knowledge anymore. :( I actually miss the cow sometimes.