Preheat oven to 350 degrees F. Lightly grease twelve 2 1/2-inch muffin cups; set aside. In a large bowl stir together whole wheat flour, all-purpose flour, wheat germ, baking powder, baking soda, and seasoned salt. Stir in 1/2 cup of the cheese, 5 of the chopped bacon slices, and the onion.
In a medium bowl combine eggs, yogurt, milk, and oil. Add egg mixture all at once to flour mixture. Stir just until moistened (batter should be lumpy). Spoon batter into the prepared muffin cups. Sprinkle with the remaining 1/2 cup cheese and the remaining chopped bacon slice.
Bake for 17 to 20 minutes or until a toothpick inserted in the centers comes out clean. Cool in muffin cups on a wire rack for 10 minutes. Remove from muffin cups. Serve warm.