Would herpes be ontop of the skin or under the skin ?

Both: Depends on what you mean by 'skin'. The eruption involves the epidermis and dermis but seldom subcutaneous tissues, although it does recur from nerve endings in the area of the eruption.

Herpes: It usually starts as a group oh pimples next to each other that later contain some clear liquid and then get crusted before they clear up. Typical location is mouth or genital area but they can appear elsewhere.