The water conditioner just removes the chlorine and a few other nasties from your tap water. The ammonia problem is due to the concentration of ammonia in your water. As you have done a complete water change, it should be down to 0ppm until you add the fish back in and they start producing more. BUT by doing a complete water change, you will have lost most of the bacteria that break down the ammonia, so if you left it now, the levels would skyrocket again, so you need to do daily partial waterchanges to keep the concentration down. In time, the bacteria will multiply enough to be able to break down all what the fish produce, but until then, lots of partial waterchanges I'm afraid!!