How I understand the question:
Humans are composed of molecules. Is there an entity, John, that overlaps each molecule additionally to all the molecules (that hes made of)?
Different answers depending on your view of the world:
Nihilism: No, there are just the very small things, probably smaller than molecules (quarks etc.), and those are the only things that exist. If there are bunches of matter, we only count all the little things the bunch is composed of, and not the bunch. According to the Nihilist, strictly speaking, John does not exist, there are just mereological atoms arranged John-wise.
Van Inwagen-Nihilism: Everything is either a small thing without proper parts (probably quarks etc.) or a living thing. According to this view, John exists, but your chair does not. One result here is that existence (as identity) is vague.
Monism: There is just one thing, The Universe, which has no parts. It is a 'seamless one'. And therefore John does not exist. The Universe is just John-ish there-ish.
Classical Mereology: John exists, tables exist, chairs exist...But also the thing composed of your nose and the Eiffel-Tower does exist. Here also problems with existence and identity arise. The ship of Theseus, the gold statue that is melted, Cats whose tails get cut off, to name a few.
*Note that these are big theories summarized in just a few words. If something sounds very stupid or more interesting, just look for more e.g. in the SEP