This article explains that there are actually three parts, not two. Excerpts:
The Tur (OC 207) explains that this berakha consists of three distinct
parts, almost like three separate blessings:
First, we acknowledge that HaShem provides the needs of all souls, of
everything He created. “Who creates many souls and [fills] their
deficiency”, that is, provides for their needs.
Second, we thank Him for everything He created in order to enliven us.
This includes enjoyments which are not in the category of a need or
lack, but rather are pleasures which enliven us. “For everything He
created, in order to enliven all living things.”
Finally, we acknowledge that HaShem is the “life of the worlds”.
Indeed, according to the Yerushalmi (Berakhot 6:1), the body of this
blessing says merely: “Who creates many souls in order to enliven the
soul of every living thing.” Here it seems clear that the term
“nefashot” or souls refers to the food we eat. According to the
Yerushalmi’s wording, the blessing explicitly refers to the hidden
spirituality present in all permissible pleasures of this world; and
even the customary wording implicitly hints at this spirituality and
soulfulness.
Secondly, the plain sense of the wording suggests that we are thanking
God for our deficiencies! We interpreted this as thanks for filling
deficiency. Yet the concepts are related, for we get a sense of
satisfaction from eating only because we feel hunger. And on the
spiritual level, we are able to assimilate and absorb the “souls” of
the permitted food only because they correspond to a particular
spiritual hunger, which we have exactly because of our “deficiency” –
which is just another way of saying a potential for growth.
The second part of the berakha continues in the same vein, referring
to the ability of God’s creation to enliven and invigorate us
spiritually – to enliven the soul of all living things. Again, the
emphasis is on the ability of material pleasures to provide spiritual
sustenance. Rebbe Natan of Breslav explains that this is why we give
precedence in blessings to foods we like better: our personal likes
and dislikes testify to our spiritual needs.
The closing of the blessing refers to HaShem as “the life of the
worlds”. In the mystic tradition, this particular appellation refers
to that aspect of God’s providence that provides an interface between
the material and the spiritual worlds. (See for example Zohar Chayei
Sarah I:132a.) It is through this interface that the material world is
enlivened, for without spiritual force from on high the world would
wither instantly.