Once a few have died then you put the carbon back into the filter to clean up the toxins that are released from the flatworms when they die.
I just want to chime in here, because I don't believe that they are toxic upon death as suggested on some sites. Some people have had issues with crashing their tanks using the product, but I believe its caused by an ammonia spike due to the huge amount of die off.
If you see hundreds in your tank, then there are thousands more hiding. The best bet is to siphon out as many as you can before you treat the tank. This will help to reduce the amount of die off that occurs after treatment, and the resulting ammonia spike.
We used a standard 1/4" tube with the plastic part of a pen attached. (we took the pen apart so we had a rigid tube). We then ran the tube into a fine mesh bag in the sump and started a siphon from the main tank.
This allowed us the ability to spend quite a bit of time sucking them out off the rocks, sand and even floating in the water column without losing any water.
Once we got as many as we could see, we treated the tank as instructed. They start to die immediately, and we started the process of siphoning out the dead ones as they started to float. After the specified duration of time, we added carbon, did a water change and nothing seemed affected by the process.
It took us 3 or 4 treatments to rid the tank as well. We tried a nudi and a wrasse before biting the bullet. I believe flatworm exit is the real way to go to fix the problem.
HTH.
It didn't really bother my corals too too much but I did do a water change after each treatment to help.
