Namakaram
Based on what i have heard from acharayas and what I have read from books, it is stated that Bhagawan expands into supersoul into every atom. This expansion of Bhagawan is known as super soul. He is one person Bhagawan who resides in spiritual world but also expands himself as super soul into every atom in this material world.
super soul is referred to as paramatma in tamil/sanskrit.
He also accompanies the individual soul in his journey in material world.
So in our heart, where the soul resides , the Paramatma also resides there , like two birds sitting in a tree. We are the one who are doing karma and eating the fruits of the tree (body). The other bird super soul just watches us and gives permission and patiently waits when we will look up to Him.
Supersoul is also present in non-sentient , acit , (non- living beings) but there is no other separate individual soul in acit.
But since the supersoul present in all atoms is the same person, Bhagawan when the material energy transforms it does not affect the same individual person, in fact the transformation can occur only under his permission!
Hope it clarifies your question.
Adiyen