levon15 - To my knowlage FWE does not directly kill other desirables in the tank, unless you overdose it.
The real problem is that flatworms have toxic "juice" in them, and if you cause a mass die off (IE kill them with FWE) they will start to release those toxic fluids into your tank. That is why the instructions ask you to siphon out as many of the flatworms as you can see, treat the tank, then (oh man I forget the rest of the instructions!!!!!!!!!)
Anyway, if you follow the directions in the package 99.999% of the time you won't have a problem. I've used it in my 120, my 75, my wife's 24 nano, and a 10 gal QT tank all with no problems. (yea yea I know, I should have had the QT tank setup sooner to prevent the flatworms in the first place, leason learned)