When you use the chunk of fish or the flakes it takes time for them to break down into ammonia in the water so yes when you use ammonia it skips that step and goes right to step 2. It saves quite a bit of time as one of the longest steps is the formation of ammonia step. The trick is to find pure ammonia. For some reason, it now is mostly scented or treated with detergent and not to be used. I found some here in a hardware store where they sold a very few cleaning supplies. They had such a low rate of turnover that this bottle probably predated all the "improvements" they have done to the good old-fashioned ammonia of days gone by. If you can find the ammonia and an eyedropper then by all means, do try that method as no only is it quicker, but there is no mess in your tank to clean up. It will leave your tank clean looking not all gunked up with fish particles or rotting flakes. But, if you cannot find Unscented Ammonia with no detergent added then you are doomed to use one of the other methods. I would probably go with the flake method before the fish as I can only imagine the smell of the fish rotting in the tank. WHEW!!!