Jewish law since the 16th century is based on the Shulchan Aruch. The Shulchan Aruch in turn is based on the Tur which is based on the Misneh Torah which is based on the talmud.
This is the chain of halacha. Now the kabala is a mystic tradition which was not known to most of the Jewish people. The rule was that when we have a conflict between the halacha and the kabala we always go by the halacha. However, the kabalah of the Ari completely obliterated this principle and many people who follow the kabbala today like the sephardim and the chassidim seem oblivious to the non-halachic nature of their customs.
Now with the ingathering of the exiles, in the last generation the bucharian and iraqui (Edot Mizrach) are tending to merge and new siddurim try to reflect everyone's way of doing things. I saw the following statement last week.
One should stand when putting on Tephillin. That is the halacha and we follow the poskim (halachic deciders) over the kaballists. However, it you follow the Ari, you can sit down to put on tefillin.