According to one reading of the atomic hypothesis it is parts that are fundamental and they tell us what wholes are, and in fact, what wholes are possible. For example:
A tree is made up of roots, trunk and branches.
A house is made up of floors, walls and roofs.
A sentence is made up of words, and words are made up of letters.
What about a theory? Is a theory a whole or a part? What is the relationship between facts/observations and theory? A good theory places the facts of the world in a web of relationships and by this we see how they all hang together and point to each other, and also by this we can predict which facts are missing or predict new facts.
This suggests, that in a sense, facts/observations are parts of theories and that a theory is a whole. But in a sense only. There is a great deal of difference between actual wholes, like trees and houses and conceptual wholes like theories, and likewise with their parts. Though there is a family resemblence.
Now, Einstein in later life told Heisenberg, in opposition to what he first believed as a young man and a young physicist, that it was the theory that tells us what we can observe.
Does this suggest that Einstein is saying it is the whole that comes before the part in opposition to the presuppositions of atomism?
It might be fruitful to ponder the following remark in relation to the above by the German philologist, Friedrich Ast
The foundational law of all understanding and knowledge is to find the spirit of the whole through the individual and through the whole to grasp the individual
This is a remark that ancestrally informed the notion of the Hermeneutic Circle, and this seems to be apposite, at least to me, to Einsteins concerns.