have you done everything such as cycle the tank?
This might go straight over your head if you haven't read the cycling or nitrogen cycle threads.
Ammonia will sit in small pockets of water if there is no agitation in the water and it will sink to the bottom of the tank, water turbulance will help drag this through the filter and across the bacteria and detoxify it (read nitrogen cycle). You can also use power heads to move and break up these ammonia pockets then the filter can take these across the bacteria.
any more infor please ask