All poskim agree that the parshi’os in tefilin need to be written in the order they appear in the Torah (קדש first, והיה כי יבאך second, שמע third, and והיה אם שמֹע fourth). There is a disagreement between Rashi and Rabeinu Tam regarding the order of the placement of the parshi’os into the batim. Rashi holds that the parshi’os should be placed in the order in which they are written. According to Rabeinu Tam, the last two parshi’os are switched so that והיה אם שמֹע is placed third and שמע is fourth (even though they are written in order). A standard pair of tefilin follows the opinion of Rashi. Some people (mostly chasidim) have the custom to also put on an additional pair of tefilin which follows Rabeinu Tam.
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STAM 101 introduction & index