Shabbat Chanuka that occurs on Rosh Chodesh (such as this year) is one of only 3 occasions that we use 3 Sifrei Torah on a Shabbat or Chag. From the 1st Torah, we read the weekly Sedra of Miketz. From the 2nd Torah we read from Parshat Pinchas about Shabbat & Rosh Chodesh; from the 3rd Torah, we read the Chanuka portion "Bayom HaShishi" from Parshat Naso. Rosh Chodesh reading precedes that of Chanuka because of the Halachic principle, "That which is more frequent takes precedence (Tadir V'she-ayno tadir, tadir kodem). Nevertheless, the Haftora (Roni V’Simchi from prophet Zecharyah) is that which is read on Chanuka & not Rosh Chodesh since it references the Menora, & is connected to the reading of the 3rd Torah, & also because the principle of "Pirsumei Nisa" (publicizing the Chanuka miracle) takes precedence over all else. Kaddish is said after the 2nd Torah reading, because Kaddish can be said on Shabbat only after 7 Aliyot have already been read.