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

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.