Yeah they can appear in any genital area of the body, covered or not.
Genital ulcer diseases and HPV infections
[B]Genital ulcer diseases and HPV infections can occur in both male and female genital areas that are covered[/B] or protected by a latex condom, as well as in areas that are not covered. Consistent and correct use of latex condoms reduces the risk of genital herpes, syphilis, and chancroid only when the infected area or site of potential exposure is protected. Condom use may reduce the risk for HPV infection and HPV-associated diseases (e.g., genital warts and cervical cancer).