The nitrifying bacteria will not show up as a dark green color on filter media. The bacteria is microscopic and invisible to the naked eye. Dark green on the filter media is usually an indication of algae.
If you are using filter cartridges that contain carbon they should be replaced every 30 days so that carbon is always fresh and working to absorb the pollution from the tank water.
Finish the current medication treatment, do your water change after, get carbon back into the filter, and let me know if you have seen any improvements within 24 hrs after treatment ends. If not, that is an indication that the medication used was ineffective and will call for something more appropriate to your situation.
As for the PetSmart issues... I can't warn enough people away from those stores. Unfortunately people shop there because they are cheaper than the smaller, private run mom & pop types of stores. The reason they are cheaper is because their staff lack the knowledge to really be of any help to the customers, lack the knowledge and experience in caring for these animals, and because they tend to buy in large quantity to sell fast from crowded tanks that have inadequate care. Another problem common with the PetSmart stores is the way their fish systems are put together. The walls of cubed tanks all share 1 common filtration unit, which is most often lack of any media. These fish are all sharing the same diseases, illnesses, parasites, etc that may come in with 1 particular fish or species of fish, simply because all of their water is cycled through every tank during the course of every day. Many species of fish need different temperature settings, yet these walls of cubed tanks can offer but 1 common temperature unless a heater is put into each cube. Take a look next time you decide to visit one of these stores and count how many heaters you see in any of those cubed tanks. These stores have many many issues and the only way we, as customers, can put a stop to it, is to demand better quality in animals. This means stop spending money in stores who are selling sick and/or neglected animals.
If these stores spend money to bring in sickly fish, or the fish are getting sick while at the store, the store is not going to care much as long as those fish sell quickly. The faster they sell the more money the store makes. If, on the other hand, they get sick fish and are stuck having to care for them, feed them, clean them, and take up tank space... until the fish die, then the store loses their money and makes nothing. That leaves the store with 2 choices. 1. either step up their care of the animals and pay closer attention to the quality of animals they are bringing in and offering for sale, or 2. stop selling the animals. Either way, the consumer and the animals both win. We need to stop lining the pockets of the people who do such an awful job and inservice to the customers and animals alike.
Mom & pop shops may cost a bit more, but more care and knowledge can be found in most of them than in the large chain stores. They take better care of their animals because that is their source of income. They understand the concept of "the most expensive animal is a dead one".
I would suggest you find a better/different place to purchase your fish in the future. When you shop for fish, do not accept sick or obviously unhealthy animals. If 1 fish in a tank is sick, it is likely that all fish in that tank are sick, as they have been directly exposed to the illness at hand. When you take that sick fish home, you then expose your fish and your entire aquarium to that illness, which often results in the infection of your other fish that were previously healthy.
This is also one reason why some of us preach so endlessly about setting up quarantine tanks. Any new fish going home should spend the first 2 - 3 weeks in a properly set up quarantine tank before being added to a main tank. If, during that quarantine period, the fish shows signs of illness, it is much easier and safer to treat that fish in quarantine and not have to risk your healthy fish with either illness or adverse effects to medications. The quarantine also allows us to suggest meds that are most effective for the sick species of fish without having to settle for one less effective due to other species in the tank that can't handle the needed medications.
Can you provide me with a list of all species of fish in this tank please? I will need to know this to be sure the medications I suggest for you are safe for all of your fish.
What size tank is this? What type of filter are you running?