I had a huge problem with aiptasia a while back. You definately don't want to let them go as they will certainly take over the tank. I got so frustrated trying to kill them with aiptasia X that I ended up taking all the live rock out and replacing it. I heard good things about the Berghia, but never tried it. I let the infested rock dry out for a few months and then slowly added it back in. I also added an Aiptasia eating file fish to my tank which I think has helped control the noxious weed from coming back.