“It is not that the individual jiva is within every atom, but Paramatma is in each atom. It is stated in the Brahma-samhita as follows: andantara-stha-paramanu-cayantara-stham, “Who is situated within every atom’”.
(Srila Prabhupada's Letter to Dhrstaketu dasa, 14th October, 1073)

“Regarding your question about the jiva soul in the heart and the jiva soul within the cells, they are separate. Both are jiva-atmas, but a particular jiva belongs to a particular body. There is the jiva in this body, but there are also jivas within the cells. Just like I am living within this apartment, but does it mean that no other living being can live here. There are so many ants, flies, bugs, they are also living within the apartment. Even in my stool there are thousands of living entities.”
(Srila Prabhupada's Letter to Svarupa Damodara dasa, 23rd June, 1973)

“Regarding your question about the difference between the mind and the soul, in the Bhagavad-gita it is directly said that the mind is inferior energy in a subtle form, and soul, jiva, is the superior energy. So they are completely distinct. Mind is not spiritual, but mind is a subtle material form. When the soul becomes captivated for enjoying the material world instead of rendering service to Krishna, that is the beginning of his fall-down. When the living being thinks himself to be the enjoyer, that is called false ego. His constitutional position is to serve Krishna. So this false egotism degrades him to pollute the intelligence and the mind.”
(Srila Prabhupada's Letter to Prema Batra, 28th September, 1975)

“You mention about the well-renowned psychologist at Harvard who is interest in finding about man’s true nature. Man’s true nature is to render service to Krishna and as soon as the living entity misuses this marginal position, he becomes conditioned by material nature.”
(Srila Prabhupada's Letter to Srutadeva dasa, 30th October, 1976)

“Regarding your questions about how and from where did the conditioned souls fall, your first question—if someone has a relationship with Lord Krishna on Krishnaloka, does he ever fall down? The souls are endowed with minute independence as part of their nature and this minute independence may be utilized rightly or wrongly at any time, so there is always the chance of falling down by misuse of one’s independence. But those who are firmly fixed up in devotional service to Krishna are making proper use of their independence and so they do not fall down.”
(Srila Prabhupada's Letter to Jagadisa, 25th April, 1970)