the bacteria is on every surface in the tank, including in the filter, but here's the kicker there is a set amount based on how much waste there is for the bacteria to feed on. if there isnt enough waste for the bacteria to feed on it dies off to a level where there is sufficient waste for it to feed on. where the bulk of the waste is, is where the majority of the bacteria will be found. so you will likely find the substrate has a good portion of the bacteria, inside a canister, or hob will likely be next in line, then everything else will have some. bacteria multiplies very fast, so if you want more bacteria, lightly over feed.