>I was hoping to make comb honey but I read that if I use Apistan it will get into the wax.
It's probably already in the wax if you use foundation. Then it gets in the wax when you use the Apistan. Then the bees move the wax around all the time...
> This is true only if I have the supers on when I'm treating them right?
It will be in the wax from the start. The only way to avoid that would be to not put foundation in the hive and not use any chemicals.