I’m assuming that what you’re asking about is the secret that Joan told Charles to convince him that she was truly sent by God, not a secret meeting between them (since this secret was delivered at a meeting that occurred out in the open). To quote Régine Pernoud and Marie-Véronique Clin in their biography of Joan Joan of Arc: Her Story (translation by Jeremy Duquesnay Adams) “What did Joan tell Charles? It is not known exactly.”

Joan’s confessor, Fr. Jean Pasquerel says that it was a secret known only to Charles and God, but doesn’t indicate what the secret was. According to the chronicler Pierre Sala, Charles’ chamberlain reported that she repeated a silent prayer that Charles had made “in his heart” in which he asked for God’s protection, and specifically to spare him from imprisonment by the English.

Other sources which were much further removed from Charles have claimed that Joan revealed she was Charles’ illegitimate half sister, a claim that keeps reappearing over and over again down through the centuries(!). However, this contradicts Joan’s sworn testimony at her trial, depositions from neighbors, etc which all indicate she was born of Jacques Darc and Isabelle Romée in the village of Domrémy. Thus serious historians reject the hypothesis that she secretly claimed to be Charles sister or any other person of noble parentage. Other theories, such as that she revealed one of Charles’ secret sins, or a password, or anything else, have no textual backing from any sources. So this brings us back to the beginning “What did Joan tell Charles? It is not known exactly.”

Your other question can’t really be addressed from a historical standpoint. There’s no way for a historian to say how she knew what she knew outside of what the sources say. We can report that she says that God was leading her and revealing secrets to her. We can report that the English accused her of witchcraft. We can’t tell you what mechanisms atheists believe enabled her to know what she knew.