I remember learning a number of different reasons as to why we eat the bottom Challah on Friday nights, and the top one on Shabbat day, but I can’t remember them. Can you please tell me the reasons?

You’re right. There are several. The most common is that the Challah we cut from represents the position of the Jewish people (who are eating the challah). At night, we are below because HaShem Who created the world is the active presence, (as emphasized in the evening davening) while in the day, when we emphasize the receiving of the Torah, the Jews are actively present, hence “on top”. At the 3rd meal the 2 challot are placed side by side to represent the harmony of Am Yisroel together with the Shachinah (divine presence).