I don't know how that worked with your old toilet, but it sure isn't the way a flange is supposed to be set. It is supposed to set on top of the finished floor, be anchored through the finished floor, and into the sub floor. Since you're dealing with cast iron, you should have a plumber remove the old flange and properly install a new one. You will have difficulty trying to do this yourself, but for a plumber, it will be a walk in the park. I advise you to spend the money and have this done correctly.