There is a disagreement between Rashi and Rabbenu Tam concerning the sequence in which the four parashiyot (sections of the Humash) are to be arranged inside the tefillin. Rashi maintains that their arrangement should follow the sequence in which these parashiyot appear in the Torah: קדש לי, והיה כי יביאך, שמע, והיה אם שמוע

Rabbenu Tam, by contrast, held that the section of והיה עם שמוע should precede שמע , as follows: קדש לי, והיה כי יבאיך, והיה אם שמועה שמע.

The Shulhan Aruch sides with Rashi’s view, which is indeed the accepted position, but adds that a G-d-fearing person should endeavor to fulfill both opinions.[177]

It is therefore customary to put on tefillin Rabbenu Tam without a berachah after the shaharit service every weekday morning, and to recite while wearing them the four sections of

 והיה, קדש והיה אם שמוע, and שמע כי יביאך  [178] 

1) If one will not have time after shaharit to don tefillin Rabbenu Tam, he should put them on after the hazan’s repetition of the Amidah, so that he can wear them during the recitation of the kedushah section in U’va Le’siyon. One should preferably not put on tefillin Rabbenu Tam during the hazzan’s repetition, since halachah requires paying attention to the hazzan. One may don tefillin Rabbenu Tam after he completes the silent Amidah if he feels confident that he will finish putting them on before the hazzan begins the repetition.[179]

2) Some have the practice of wearing tefillin Rashi and tefillin Rabbenu Tam together, simultaneously, rather than donning tefillin Rabbenu Tam after shaharit.[180]

a. One who follows this practice should wear the tefillin shel rosh of Rashi toward the front of his head, closer to his face, and the tefillin Rabbenu Tam behind it, toward the back of his head. 

The tefillin shel yad of Rashi should be positioned on the designated part of the muscle of the upper arm, while the tefillin Rabbenu Tam should be placed lower down, facing the hand.[181]

b. One should preferably ensure that the base of the tefillin Rabbenu Tam does not rest on the ma’abarta of the tefillin Rashi, or vice versa, despite the fact that this is permissible according to the strict halachah. They should instead be situated one in front of the other.[182]

c. The straps of the tefillin shel Rashi should be wrapped over the straps of the tefillin Rabbenu Tam.[183]

d. One should recite the berachah and then tighten the straps of both tefillin simultaneously.[184]

3) One who wears both tefillin Rashi and tefillin Rabbenu Tam — regardless of whether he wears them simultaneously or separately — must have in mind that he fulfills the mitzvah only with the correct pair of tefillin, and the other is not worn for the purpose of a mitzvah. If one does not have this intent, he might be in violation of the prohibition of bal tosif — adding onto the mitzvot of the Torah.[185]

4) Unmarried men should not wear tefillin Rabbenu Tam unless they feel confident in their ability to refrain from inappropriate thoughts throughout the time they wear the tefillin Rabbenu Tam.[186]

5) When one puts on tefillin Rabbenu Tam, he may not speak in between the laying of the shel yad and the laying of the shel rosh, as when donning tefillin Rashi, because the two should be placed immediately one after the other. During this time one may not even speak in matters of Torah, or answer “Baruch Hu u’varuch Shemo.” One may, however, answer “Amen” and respond to kaddish, kedushah and barechu in between the placing of the shel yad and shel rosh of tefillin Rabbenu Tam. Furthermore, if one sees lightening or hears thunder during this period, he may recite the appropriate berachah. In such a case, after reciting the berachah one should preferably touch the tefillin shel yad and tighten it around his arm before placing the tefillin shel rosh. Likewise, one who mistakenly spoke in between the placing of the shel yad and shel rosh of tefillin Rabbenu Tam should feel the shel yad and tighten it before placing the shel rosh.[187]

6) It is proper to spend some time studying Torah after shaharit while wearing tefillin Rabbenu Tam.[188]

7) If one mistakenly put on his tefillin Rabbenu Tam with a berachah before wearing his tefillin Rashi, thinking that they were tefillin Rashi, and he realized his mistake before he spoke, then he should remove the tefillin Rabbenu Tam and then place tefillin Rashi without a berachah. If, however, he realized his mistake only after he had spoken, then he must recite a new berachah when he dons tefillin Rashi.[189]

8) One who mistakenly removed his tefillin Rabbenu Tam from his tefillin bag before tefillin Rashi should nevertheless put on his tefillin Rashi first.[190]

9) One should make a point of keeping the tefillin Rashi and tefillin Rabbenu Tam in two separate, clearly-labeled bags.

Since only one of the two pairs is endowed with the sacred status of tefillin, and halachah forbids placing a mundane article in the bag designated for tefillin, one must ensure to always place each in its designated bag. However, if a bag was initially designated for both tefillin Rashi and tefillin Rabbenu Tam, he may keep both pairs of tefillin in that bag.191 Furthermore, one may keep both pairs of tefillin together in his tallit bag, since in any event the tallit bag is not designated exclusively for tefillin.[192]

10) One’s tefillin Rabbenu Tam should be smaller than his tefillin Rashi, both for reasons involving the teachings of Kabbalah, and so that one will know the difference between the two pairs and not mistake one for the other.[193]