The parasites themselves cannot live for long outside of the host organism, but the eggs (on the poo) may survive until the hatchling emerges. So, it's important to feed GC + Focus daily, and to ensure every fish in QT is eating the medicated food. Because you're basically fighting a war of attrition with internal flagellates/worms, which is why it can sometimes take so long to fully eradicate them.
It would be better to run the carbon in a media reactor, to force the water through the carbon. When you put it in a bag, some of the water will go around it.