It is important to daven the Kedusha of Uva L'Tzion with the tefillin on and with a minyan, if possible. If you must leave early, should say them whenever you get a chance. The Arizal says that when the entire davening we are asking Hashem to bestow upon us his bounty, and these blessings descend during the end of davening. So it is very important to daven until the end.
According to Halacha one may change the order of Ashrei and Uva L'Tzion if there is a need to do so, as we find when the tzibbur is up to the Kedusha one should skip from the middle of Ashrei. However, one should try to avoid such a situation, because according to Kabbala it is very important never to change the order of the tefilos.