If using the wood chips, place them in a small bowl; cover with water and soak for 20 minutes.
Add the seeds to a small skillet over medium heat. Toast until fragrant, 2 to 3 minutes. Grind the seeds coarsely in a mortar or spice grinder. Place the salmon skin side down on a plate. Sprinkle with salt and pepper, and then the ground seeds and lemon zest. Brush with olive oil. Let marinate while preparing the grill.
If using the wood chips, drain the chips, and place in a smoker box or in a disposable foil pan. If using a gas grill, place the smoker box or foil pan directly atop a burner and preheat the grill to medium-high. If using a charcoal grill, prepare medium-high coals. Place the smoker box or foil pan directly atop the coals. Cover the grill until the wood chips give off smoke, about 5 minutes.
If not using the wood chips, prepare a charcoal or gas grill for direct-heat cooking over medium high heat.
Place the salmon skin side down on the grill. Cover the grill and cook the salmon without turning over until it is just cooked through, moving to a cooler position or decreasing the heat if the skin is browning too quickly, about 10 minutes.
Meanwhile, prepare the tomatoes: Heat the oil in a medium nonstick skillet over medium high heat. Add the onion and red pepper and sauté until the onion is almost tender, about 3 minutes. Add the tomatoes and sauté until tender and starting to juice, 2 to 3 minutes. Remove from the heat and stir in the basil and thyme. Season to taste with salt and pepper.
Cut the salmon into 2 pieces and transfer to plates. Spoon the sautéed tomatoes over and serve right away.