The accepted and most common minhag is to sit while reciting the berakha and while fastening the tefilin shel yad on the arm, but to stand when affixing the tefilin shel  roshon the head. [1]

[1] Many contemporary ribis, among them Ribi Shalom Messas zs”l (Shemesh uMagen,Heleq 2 H“M §3:2), Ribi Yedidya Monsonego (Pirhé Shoshanim §400), and Ribi Yehoshu’a Maman (‘Emeq Yehoshu’a, Heleq 3 § 31), have confirmed this to be the accepted minhag, and that in Morocco this was always the custom of Tora scholars and those who were careful about halakha.


[2] This minhag is really a compromise between halakha, which recommends standing when fastening the tefilin shel yad, and Qabala, as the Arizal instructs one to be seated during this time. This minhag is mentioned in the sidur Bet ‘Obed (Laws of Tefilin §27) and by the Rama (O”H §25). It is a fairly common minhag and was the prevailing custom in the city of Tetouan.


[3] This practice was widespread among laymen (see Ribi Yosef Messas zs”l in MayimHayim, Heleq 2 O”H §93); yet, they were not rebuked by the ribis (Ribi Shalom Messas  zs”l in Tebuot Shemesh Heleq 1, §67), making this practice perfectly legitimate from ahalakhic standpoint. Nevertheless, since this was not the practice of Tora scholars, I hesitate to give it the status of a bona fide minhag.