There are several references to our having two rather that just one Nephesh. “One of them derives from the klipah and sitra achra (i.e., the side of un-holiness). It’s clothed in human blood and gives life to the body“, while the second is “a veritable portion of God Above (Sefer Tanya Ch’s 1-2, based on Eitz Chaim 3:2). The latter is obviously “holy and not from the sitra achra” (Zohar 1, p. 13a).
The Nephesh is said to be correspond to the Holy Ophanim, as opposed to the Neshama and Ruach, which correspond to the Seraphim, and the Holy Chayot (Tikkunei Zohar Chadash 96a; also see HaRav m’Fano’s Ma’amar HaNephesh 4:3).
“The Lower Shechina (i.e., the Sephira of Malchut, as opposed to that of Binah which is the Upper Shechina) that was granted to man is the Nephesh Sichlit (i.e., the rational soul, which was granted to us) in order to know all the ways of Torah” (Zohar Chadash, Yitro p. 33b; also see Sefer Tanya Ch. 3 for more on the Nephesh Sichlit).
“Those who engage in Torah study inherit a vital Nephesh (i.e., their life-force) from the Shechina” (Tikkunei Zohar 45, p. 82b), and “they (thus) rectify their holy Neshama (Introduction to the Zohar 12b, also see Ra’aya Mehemna, Pinchas p. 42b). And “those sages who study a lot of Torah inherit (a reward) from their vital Nephesh source (Tikkunei Zohar, 47, p. 83b, Hashamatot Breishit p. 52b).