The procedure of this mitzva is as follows: The Kohen Gadol entered the Kodesh Ha-kodashim with a panful of glowing coals and a ladle of incense. In the Kodesh Ha-kodashim, he scooped out two handfuls of incense which he placed on the coals. The smoke rose up, mushroomed, spread out through the Kodesh Ha-kodashim, and ultimately concealed the kaporet, as we read, “He shall take a panful of glowing coals scooped from the altar before the Lord, and two handfuls of finely ground aromatic incense, and bring this beyond the parokhet. He shall put the incense on the fire before the Lord, so that the cloud from the incense screens the kaporet that is over [the Ark of] the Covenant, lest he die” (Vayikra 16:12-13). This indicates that even the holiest member of Israel could not comprehend God as He truly is. The Shekhina appears only within smoke and fog, and through the fog, the divine idea is progressively revealed. Therefore, the Kohen Gadol first had to offer incense in the Kodesh Ha-kodashim, and only once the Kodesh Ha-kodashim filled with smoke could he fulfill the mitzva (Yoma 53a).
Since the incense expressed the deep bond between God and the souls of Israel, the firepan of incense remained in the Kodesh Ha-kodashim until the day’s avoda was completed. That entire time, its smoke continued to rise. Upon completion of the avoda, the Kohen Gadol entered the Kodesh Ha-kodashim on behalf of all of Israel, picked up the shovel, and departed.
The Kohen Gadol offered two handfuls of incense, no more and no less (ibid. 48a), alluding to the idea that all his actions and intentions were devoted to klal Yisrael. The Sages tell us that scooping a handful of incense out of the ladle without spilling a single grain was among the hardest jobs in the Temple (ibid. 49b). This alludes to the idea that the Kohen Gadol must try to bind all the energies of Israel to the Kodesh Ha-kodashim without losing even a single spark.
The daily incense was finely ground, but the incense offered by the Kohen Gadol in the Kodesh Ha-kodashim on Yom Kippur was pulverized further to make it superfine. Grinding enables the unification of all the individual particles, and the incense offered in the Kodesh Ha-kodashim had to express a deeper unity.