Forgetting about floating and sinking, which are macroscopic issues, the definition of density is the same on any scale.
Density = Mass per unit volume
You get the same answer if you are dealing with a bucket sized sample or a single, whole molecule. Looking inside a molecule, the Mass is not distributed uniformly so the dense bits will be the nuclei and there will be ( mostly) empty space in between occupied by some electrons.
When your substances are fluids, on the ground, the more dense substance will fall down and displace the less dense. That is a universal rule unless there is some chemical reaction between the two substances.