Already: implies you go on a lot of trips, and your mother is wondering whether or not you have been there already, most likely because she doesn't know if you have. Already deals with past occurrences in that there's a hypothetical list of things that the speaker is ticking through as they speak to you. As in, "She's been to Argentina, Brazil, Comoros, and Burkina Faso, but she hasn't been to Chile - has she? I should ask to find out."
Yet: implies that you don't go on a lot of trips, and your mother is wondering whether or not you have been there already, most likely because she doesn't know if you have. Yet deals with future occurrences in that you could have gone somewhere before, such as Argentina or Brazil, but you haven't yet gone to Chile - and these locations together formed a list of places you were supposed to go. Perhaps Chile is your last stop. Perhaps the other countries are. The list isn't specified in the speaker's mind. As in, "She's said she's going to all these places, but what about Chile? [she knows you're supposed to go there, but doesn't know if you're there now or when you're supposed to go]"
Hope that helped.