Preheat waffle iron. In a large bowl, combine the flour, baking powder, baking soda, salt, oregano, basil, red pepper flakes, and and whisk until blended. Add the daiya and bacon bits and mix to coat with the flour mixture.
Add the almond milk and oil to the dry ingredients until just combined, taking care not to over mix.
Grease hot waffle iron. Pour about 1/2 cup batter into the waffle iron and cook 3 to 5 minutes, or until waffles are golden and cheese is melted. Repeat with the rest of the batter. Serve with warm marinara sauce.