ולקחת סלת ואפית אותה שתים עשרה חלות (אמור כד:ה)

And take a basket and bake twelve challahs.

The reason for י”ב חלות

The Ari Hakadosh zt’’l explains why one should prepare twelve challahs for Shabbos. This is to commemorate the twelve challos that were ready for the לחם הפנים each Shabbos during the times of the Beis Hamikdash and placed on a golden table.  The challahs remained fresh from week to week.

• It says the word “שבת” twelve times in the Torah.
• The twelve loaves were placed on the table, six on each side, because the לחם הפנים brought upon the bracha of parnassah for the six days of the previous week and the six days of the upcoming week.
• There’s a minhag to make two challahs (לחם משנה) comprised of six braids each =יב חלות.
• Reb Yechezkal of Kazmir zt’’l was asked why he doesn’t place twelve challahs on his Shabbos table, to which he replied: “I have twelve challahs! I place two challahs on my table, and I am a “Yid – י’” = twelve challahs!”
• The Belzer Rebbes use twelve small challahs for each Shabbos meal, plus three large challahs, of which two are braided – referred to as a “koilish,” and one challah is a smooth loaf, referred to as a “kichen” and twelve small challahs surrounded them. 
• Maran Reb Aharon of Belz zt’’l used to distribute the twelve challahs to the students learning in Yerushalayim who excelled in their studies that week.