I have never used it in the fermenter. If you are short on headspace, you probably could although I have no idea how effective it is. Depending on what yeast, how much headspace, temperatures, you may or may not need it. If you are really worried about it, use a blowoff.
My bottle of Fermcap-S says to use it in the fermenter, I think 1 drop per gallon.
I've only used it on one batch so far, in the starter and again in the boil. The starter didn't seem to foam up at all, only a very thin layer of bubbles at best, but the yeast was certainly growing.
Also worked great during the boil though I'm not sure if it carried through to the fermenter. It looked like it made the standard 2-inch krausen head in the carboy, nothing I wouldn't expect for a 1.054 O.G.
It does work in the fermenter, but you may have to reapply it from time to time, which puts you above the recommended dosage. I have had a couple of blowoffs even after using it, but it usually does a decent job. I suspect Fermcap-S would be a better choice.