It is customary during Nakdishach to lift oneself by raising his heels off the ground during the recitation of "Kadosh Kadosh Kadosh Hashem Seva’ot." Each time one recites "Kadosh," he pushes himself upward by raising his heels.
There is, however, a debate among the authorities as to how precisely this should be done. The Ben Ish Hai (Rav Yosef Haim of Baghdad, 1833-1909), in Parashat Teruma (6), rules that each time one lifts his heels, he should raise himself a bit higher than the previous time. This ruling is based upon the famous Halachic principle of "Ma’alin Ba’kodesh Ve’en Moridin," which means that in matters of Kedusha we should always try to increase, rather than decrease. Thus, in lifting ourselves during Nakdishach, we should lift ourselves higher with each recitation of "Kadosh."
Hacham Ovadia Yosef, however, disagrees. According to his understanding of the teachings of the Arizal (Rav Yishak Luria of Safed, 1534-1572), the first "Kadosh" represents the highest level of sanctity, and therefore one should not lift himself progressively higher for the subsequent recitations of "Kadosh." In Hacham Ovadia’s view, one should raise himself to the same extent for each "Kadosh." Of course, one does not have to measure the extent of his elevation so that he lifts himself to the precise same height each time; rather, one should raise himself more or less to the same height all three times.
As for the final Halacha, everyone should consult with his Rabbi for guidance.
If a person is still reciting the Amida when the Hazan reaches Nakdishach, he should stand in place silently and listen to the Hazan’s recitation of Nakdishach. He should not lift himself during "Kadosh Kadosh Kadosh" along with the congregation. Rather, he should simply stand in place silently, listening to Nakdishach, and then continue his recitation of the Amida.
Summary: According to one view, a person should raise himself progressively higher the three times he raises himself during "Kadosh Kadosh Kadosh," whereas others maintain that one should lift himself to the same height each time. One does not lift himself if he is still in the middle of the Amida and is listening to the Hazan’s recitation of Nakdishach.