1. Stir the yeast, sugar and water together in a mixing bowl and let stand, uncovered, until a foam develops on the surface, about 8 to 10 minutes. (If a foam does not form, the yeast is dead and should be discarded.)
2. With a wooden spoon, stir in 2 tablespoons of olive oil, the whole wheat flour and 2 teaspoons of salt. Stir in the all-purpose flour by the cupful until an irregular shaped dough forms and pulls away from the sides of the bowl.
3. Place the dough on a lightly floured work surface and knead by hand, adding flour as needed to keep the dough from sticking. Knead until the dough is smooth, slightly sticky and elastic to the touch, about 8 to 10 minutes.
4. Spray the inside of a clean bowl with a non-stick spray and place the dough in the bowl. Cover with plastic wrap and lay a kitchen towel over the top of the bowl to keep the warmth inside. Let the dough rise at room temperature until it has doubled in size. This will take about 1 1/2 to 2 hours. (Or, let the dough rise slowly in the refrigerator over night.)
5. In a medium sized skillet, cook the onions with the remaining tablespoon of olive oil over medium heat until the onions are wilted, about 5 minutes. Put the onions in a bowl and set aside.
6. Turn the dough out onto an oiled cookie sheet. Using your fingers, spread the dough out to roughly a 12" X 14" shape. The dough should not be thicker than 3/4". Dimple the dough with your finger tips. Sprinkle the surface with the onions and the remaining salt.
7. Preheat the oven to 400°F while the dough rests for 15 minutes.
8. Bake the focaccia in the hot oven until it is light golden brown, about 25 minutes. Let the focaccia cool for at least 15 minutes before cutting it.Serving Size: 1 piece