There are numerous occasions over the course of the year when two Sifreh Torah are taken from the Hechal and read in the synagogue. This Shabbat, for example, is Shabbat Zachor, when we read the weekly Torah portion from one Sefer Torah, and the special section of “Zachor” from a second scroll. There are even occasions when three Sifreh Torah are read. This happens on Hanukah, for example, in years when Rosh Hodesh Tebet (which occurs during Hanukah) falls on Shabbat. In such a situation, we use one Torah scroll for the weekly portion, a second Sefer for the Rosh Hodesh reading, and a third Sefer for the Hanukah reading.
The Poskim rule that whenever two or more Sifreh Torah are taken from the Hechal, the one from which we read first should be placed to the leftmost side. The one that is used second should be placed to its right, and if a third Sefer Torah is read, it is placed to the right of the second scroll. The Shulhan Aruch rules that in performing Misvot we always begin to the left and move rightward, and thus the first Sefer Torah should be positioned to the left, with the scrolls read subsequently arranged to its right. This was the practice of Hacham Yehuda Sadka (1910-1991), and this ruling appears in the work Ner Le’siyon (Halacha 37; listen to audio recording for precise citation).
Summary: When two Sifreh Torah are taken from the Hechal, the one from which we read first is placed to the leftmost side, and the one that is used second is placed to its right. If a third Sefer Torah is read, it is placed to the right of the second scroll.
