Actually you're right about the bacteria colonizing everywhere in the tank. I'm still seeing some side effects. My cheato barely grows which leads me to believe that the organic content is still low, despite the fact that I feed every day and twice a week at night. The skimmate from my skimmer is also still very dark and smelly, which is a by-product from bacteria systems (pellet users have the same experience). So the bacteria are still in there and the torpedo was turned off almost a month ago.

With a smaller setup like yours you'd probably get by with seeding the system with a bottle of bacteria. The rock and substrate should provide adequate space for the bacteria to grow. You could even add a small bag of carbon or Chemi-Pure Elite if you think you need more bacteria. Just make sure you place the carbon where it can get adequate flow.