This is a specific hpv (there are about 40 different ones) that effects only the genitalia (and back of the throat in extremely rare occurences). The cream is to remove the warts themselves, but remember, this is in your system forever as it's a virus. After they are gone, a lot of people don't have them show up again and some have infrequent outbreaks. A lot of people who have it don't ever show signs of it. If you do have another outbreak, each one becomes less severe and farther apart in time.
Hpv is very body position specific. You can't get genital warts on your hands as you can't get planter's warts on your vagina, etc.
They can be treated in other ways if the cream is too intense. They can be frozen off, which hurts, but the results are very quick and over with.
Go back to you doc.