Inside the fence that surrounds your dog yard, try not to grow any plants in the area immediately adjacent to the fence. Dogs like to investigate things outside the yard, and their favorite path in a fenced-in yard will be right along the fence. Unsightly "dog paths" are the result of this predictable behavior.
Rather than fighting it, plan your yard around your dog's predictability. Install stone walkways over existing dog paths. Now everyone will be happy: the dog still has its path, and you get to have a better looking yard. Stone walkways exude charm and are a desirable addition to your landscaping regardless of dog problems. DO NOT USE COCOA MULCH - it attracts dogs and is HIGHLY toxic.
Your beautiful back yard with the trees, flowers, grass and vegetable garden may seem like paradise to you, and your dog will certainly enjoy romping around back there, but there are safety considerations as well, and you will want to make sure your tender plants are protected from your dog.
Dog resistant plants are textured or thorny. For obvious reasons, dogs do not like thorny plants, such as barberry or evergreens. Unusual textures also deter dogs, like lavender or rosemary. Many of these plants are beautiful winter features which can also be planted in front of the dog’s bathroom creating year round beauty and hide their waste.
You'd be surprised at how many of the most common landscape plants and native volunteers contain at least some parts (leaves, berries, etc.) that are toxic. Consider carefully what you plant in your yard. Plants that can cause complications include: Rhododendron, Japanese Yew, Lilly of the Valley, Peach and Cherry Trees (pits) to name a few.
Dogs love to dig. Some breeds, in fact, simply have to dig. For them, it is part of the joy of being alive. They don't care if what they are digging up is a prized flower garden or the spinach crop you have been carefully tending since early spring. And a dog doesn't at all mind taking a short cut through the flower beds trampling them as he goes. You may want to consider fencing off areas of your yard to protect your plants. This is particularly the case with frisky young pups. As your dog grows you will be able to train him to stay out the flower or vegetable garden, but to a puppy, it all looks like a playground.
Dog Behavior Modification: Another option is to train your dogs so as to restrict their "toilet space" to a designated area. To facilitate clean-up, make sure that designated area has a surface of dirt or gravel. Start on day one by taking your puppy IMMEDIATELY to this "place" you want him to use. As soon as he pees or poops, praise lavishly and reward him at the right place. Soon he will learn that the praise comes when he does his business there, but not anywhere else. My dogs all go to the back corner furthest from the house. Makes clean-up chores much easier!