The exact phrase you ask about, "כשהוא שוחק אומר הדק היטב היטב הדק" is on kritot 6b following a Tannu Rabannan in the name of Abba Yosi ben Yochanan. So if you are only trying to cite that phrase, you could say כריתות ו:ב ד״ה ת״ר היו מחזירין which would put you at the spot on the page.
The Yerushalmi Yoma, chapter 4, halacha 5 in the Gemarra brings the added idea that the sound of the voice is good for the preparation in the name of Rabban Shimon ben Gamliel.
That detail is brought in Bavli in the name of Mar from the support of Rabbi Yochanan.
For what it's worth, I don't see any source (Bavli, Yerushalmi or Midrashim) other than the siddur which actually cites Rabbi Natan with this statement. That could suggest that either it was a variant text which ultimately wasn't used in Mishah and Gemarra or that there is a halachic midrash that no longer exists. A search of the Tosefta also comes up empty. As is known from Horayot 13b, Rabbi Natan's name was to a large extent removed from the Talmud.
A couple of interesting discoveries are that the Siddur of Rav Amram Gaon does not require the recital of the Ketoret at all in connection with the recital of the Korbanot. It follows what is found in the Avudraham that the Tamid is required and then the recital of Eizehu Makomen from Zevachim 85, followed by the baraita of Rabbi Yishmael from the beginning of Sifra. Amram Gaon includes recital of ketoret at the conclusion of shacharit and arvit but only in remembrance of the Temple. And the text he uses mentions הדק only in connection with the double grinding for Yom Kippur. There is no mention of the beneficial relationship between the voice and the spices.
The exact text including the citation of it being said in the name Rabbi Natan is found in Sefer Avodat HaKodesh by Rabbi Meir Ibn Gabbai, section 4 (Sitrei Torah), chapter 19 with the words beginning, "בעמדם תרפינה כנפיהם". I haven't had a chance to review the chapter but it begins by talking about traditions that were only passed down to the select individuals (in his words בני עליה). Rabbi Meir is a recognized early authority in kabbalah from Spain, born before the Spanish expulsion. He introduces the idea that the current exile was the consequence of violating several covenants, one of which was ceasing to follow the path indicated above. This has an implication about the kavanot associated with prayer. He points out that this is in addition to violating the path below, which means the mitzvot outlined in the Mishnah.
This indicates that a variant text was present at least among the kabbalists of Spain shortly after the Gaonim and was included in most of the later siddurim.
One of the interesting details to note about this is that this is supported by the work of Rabbi Avraham Katsch z"l, who headed Dropsie College in America. In the 1940s and 1950s, Katsch worked to try to recover many of the one of a kind, hand-written manuscripts and fragments which were in the Guensberg collection in St. Petersburg in Russia. Many of these were collected from Sephardic Jewish communities and genizas across Europe and they contained variant texts to the Mishnah not found in the Tosefta or Mechilta, and very old kabbalistic material including from Rabbi Yitzchok of Akko.
The Baladi nusach of the Temani Jews, which is the older practice, does not recite the ketoret for shacharit. But they do recite the ketoret before mincha and the version of their text does not include section on הדק היטב היטב הדק.
As a matter of context, the teaching of the ketoret was, according to tradition, given by the Angel of Death to Moshe Rabbeinu. It was used by Aharon, Kohen Gadol to stop the plague that resulted from the actions of Kozbi and Zimri.