She isn't trying to scare you, she's giving you some facts, the vaccine protects you from certain viruses that causes types of cancer, men can be carriers and give it to you, from their past sexual relationships. It is not effective once you've already had sex that's why they advice it to young girls before they become sexually active

The pills takes a while to be effective so use a condom until then, read instructions and follow them well ie. what to do when you miss a dose, what to do during sugar pill week

A partner can have something but not physically show it at the moment, he can have exacerbations and remissions and still pass it on. Did both of you get tested for the whole panel? It's tough thing about relationships especially at first, making sure he is monogamous. Some Infections can be treated, but there are no cures for viruses; herpes HIV. use KY jelly, not lotion just make sure you protect yourself, otherwise enjoy.