The Shulhan Aruch (O.H. 274:1) writes that upon reciting the blessing of Hamotzi over two loaves, one should break pieces off the bottom loaf to eat and to distribute to those gathered. The Rama (ibid.) adds that according to Kabbalah, one should break off the bottom loaf on Friday night and the top loaf on Shabbat day. The Bach (O.H. 274) questions this custom because it would seem that on Friday night one is passing over the top loaf in order to break off from the bottom loaf, which seems to contradict the dictum of En Ma’avirin Al Hamitzvot, that is, one should not pass up the opportunity to fulfill a Mitzvah. The Taz (O.H. 274) concurs and says that the remedy is to tilt the two loaves such that the bottom loaf is the first to be accessible for breaking off. Rabbi Ben Zion Abba Shaul (Or Lezion, vol II ch. 21, § 1) says that one should hold the two loaves side to side and hold the lower loaf closer to oneself.
Despite the Rama’s ruling, the Kaf Hahaim (K.H., O.H. 274:2) and many Mekubalim write that one should always cut the top loaf. Nevertheless, Rabbi Amram Aburbia (Netive Am, pg.150) writes that upon close analysis of the Arizal’s works, there is no mention of specifically giving preference to the top loaf. This may explain why Rabbi Baruch Toledano (Kitzur Shulhan Aruch ), who normally follows the methodology of the Kaf Hahaim, actually concurs with the Rama’s opinion. It should be noted that Rabbi Yitzhak Ratzabi (Olat Yitzhak, vol. II, § 122) says that the Yemenite custom is also like the Rama.
Summary: One should cut off pieces of bread from the lower loaf during the Shabbat night meal, and from the top loaf on the Shabbat day meal.