Forgive my uncertainty, but I assume you mean the area where the stock meets your cheek, correct? If so, then it should be fine. However, I wouldn't get bondo... I've never used it personally, but I've had good experiences with marine-grade resins in my car. You can get ones that have either long or short strands... In your case, I suspect the long strand might be better if you want to build up a base coat, and then some putty to fill in the cracks. The long strands will hold together better than just a putty and prevent it from cracking.
Your other option would be to layer a few sheets of fiberglass over your stock and resin them into place, then sand them down and paint. If you've got a wooden stock, you may consider putting a layer of aluminium foil or something over the stock, then building up the cheek piece to a height you like (without fiberglassing directly to the stock). Once you have it high enough, remove the fiberglass from the stock, cut it to shape, then sand and paint. If you include some sort of D-ring or nylon strap, you could mount it to your stock as needed, without actually modifying it. That'll allow you to keep a nice wood stock underneath, and paint the fiberglass section black, grey, red, etc.