You'll frequently read ammonia after a water change because: Most municipal water suppliers add chloramine as an antiseptic/antibacterial. Chloramine is composed of chlorine and ammonia. Any dechlorinator turns the chlorine into harmless chloride, but leaves the ammonia. Prime then locks the ammonia in a harmless molecule -- but the API test still reads this ammonia.
This harmless molecule begins to decay almost at once, and it loses most of it's protection after a day or two, depending on the amount and type of organics it's locking.
Unless and until you know your tank is cycled (0.0ppm ammonia, 0.0ppm nitrite, nitrate increasing slowly over time), it's a good idea to add a few drops of Prime every day.
How much bacteria is in the filter, as opposed to in the substrate, walls, decor, plants, livestock is a topic for a good discussion -- but it's not as simple as counting. The filter bacteria is exposed to more ammonia, so it treats more water than does the substrate. In a mature, established tank, the bacteria grows and arranges itself throughout the system to oxidize exactly the amount of ammonia produced by the livestock. And it does this in the most efficient way possible.