Water changes are your best way to manage nitrate concentration, especially since it is not just nitrate that is harmful, just the easiest thing to test for.
You can definitely put other medias in the cartridge that holds carbon. A true media reactor uses a specific flow rate to prevent the media from being broken apart or sitting stagnant. I am assuming this is freshwater since you said something about a nitrate removing media. Depending on the fish you have and your water chemistry you could stick some crushed coral in there to help keep the pH/KH
up if necessary.
The polishing cartridge is not made to be used all the time, it is designed to be put in for a few hours to polish the tank on occasion.