Why do we make Hamotzi on the lower of the two Challahs on Friday night and on the upper one on Shabbat day? Thank you.

ב"ה Shalom Cutting the lower challah Friday night is based upon Kabbalistic reasons. (בית יוסף , או"ח סי' רע"ד). Following the regular rules of Halacha we should be eating the Challa which we encounter first which is the top one so as not to "skip over " a mitzva and therefore that is why we take from the upper on Shabbat day when the Kabbalistic reasons don't apply. (Also on Yom tov the upper Challa is taken.) Due to this halachic ruling, the custom is to have the lower Challah a bit closer so we don't skip over the closer mitzvah, or there is the custom of making Hamotzi while holding the Challa on top and then placing it on the bottom just before cutting it. All the best