So this is an indoor herb garden? The gnats thrive in situations of consistent moisture and not enough air circulation. So if your herbs are not seedlings best is if you can let the herbs dry out pretty thoroughly between waterings and make sure the potting soil is free draining, like cactus mix. Many herbs prefer those conditions anyway.
But yes you can use the chamomile and cinnamon together. And yes, it needs to get in to the soil, not just sit on top. I generally put the cinnamon (it just takes a little) in the water I am watering with to help it soak in.
I have found it very effective at keeping fungus gnats out of my indoor seed starting operation. It does not work instantly. It is not a poison. It is anti-fungal, so works against the fungus in the soil that the adult gnats eat. So after awhile, there is nothing to eat, they go away. But if there are eggs in the soil, new ones may keep hatching out for awhile.