From what I understand, and by using a mathematical metaphor, everything manifests like: 0, 1, and n.
Krishna, thus, exists in unmanifest form, but manifests as Balarama (Sankarsana), Who then proceeds to create the world of plurality. Yet, when the world is about to end, Sankarsana begins to draw the multiplicity together into a united whole (hence His usage of a plough and His name). Once the entirety of plural existence has been organized into a whole, this whole is then subjected to the Original God (Krishna, the 0), and the souls of the jivas thus exist within Krishna in an unmanifest form for a time (as "seeds").
Sankarsana continues to exist outside of Krishna as Sesa, the sole part of Vishnu that exists outside of Vishnu during the pralaya, hence His name, the "remainder." (It appears that Lakshmi continues to exist outside of Vishnu as well.)
This is the manifest perspective of the whole lila. But it appears to leave no location for a Moksha-ed soul to exist.
Reading some answers and comments from this question: What will happen if all souls inhabiting Earth attain Moksha?
My understanding is that a person who attains Moksha simply exits the entire play and perceives it to be an illusion. The only reality this person sees is Brahman (ultimate non-dual reality). Everything else is Maya, for this person. The question of the existence of other people, the pralaya, the end of the world (the yuga), of birth, and of death, simply ceases to exist.
This must ultimately mean that the appearance/existence of Krishna, of the pralaya, the cycle of yugas, the existence of Sankarsana/Sesa, even the existence of God, must be a complete illusion for someone who only perceives Brahman.
Given these two ideas, I have no choice but to conclude that God only exists in Samsara as Maya, this God-in-Samsara-as-Maya, appears as Krishna (the highest form of God). Krishna of course, appears with His expansions, Balarama and Radha, and Whoever else.
But for a Moksha-ed person, the entirety of the manifestation, including the apparent-manifestation of God is also transcended, leaving apparently, nothing.
So is theism in conflict with liberation?
It seems so from this perspective.