There are no such things as "atoms". There are only protons, neutrons, and electrons. A hydrogen atom is composed of one proton and one electron.
But there are no such things as "protons," either. There are only quarks. A proton is composed of two up quarks and one down quark.
And so on...
Do we really believe that? Of course not.
Atoms have their own existence and emergent properties that arise from their constituent parts. Atoms can join together to form molecules in ways that are too complex to describe in terms of protons, neutrons and electrons. And if we tried to explain them in terms of all their underlying quarks, we would be lost.
There is no deterministic relationship between levels. Electrons are probability waves until they exist as particles. The complex folding structure of proteins can't be fully determined by the underlying components, because there is always quantum uncertainty. One level is a statistical aggregate or description of the lower level, but you can't predict what each individual part contributes to the whole.
Once a "higher" explanatory level can describe emergent properties and behavior with more elegance and simplicity than lower levels, and, more importantly, those higher properties are stable across space and time, then the new explanatory level becomes useful. It comes into its own existence.
A molecule has its own existence, over and above the existence of its constituent atoms and quarks, because it has stable properties and stable interactions with other molecules in ways that cannot be elegantly described in terms of its underlying parts.
Human society is yet another level, with its own rules that explain the mysterious workings of matter at a higher level. Society exists because it has stable properties across time and space, and terminology (culture, psychology, wants, desires, ambitions) that explain matter more elegantly than a purely reductionist description in terms of physics and chemical reactions.