Although chemists are accustomed to representing the atoms within molecules by spheres, it is still a task which can be accomplished in many different ways.
The most rudimentary is the so-called ``ball and stick'' model, which can even be realized with gumdrops and toothpicks. All atoms have are taken to have the same size, but do not fill space. In that sense, they represent the nuclei, separated at distances taken from crystallographic data, for example.
When electrons are also taken into account, an atom can be assigned a radius corresponding, say, to where 90% of its electrons are to be found. In this presentation, atoms overlap (bonding can be attributed to electron pairs occupying the same region). Mechanical models traditionally slice away parts of the sphere at stereotyped bonding positions, still maintaining some flexibility of interconnection.
Elaborate model kits maintain variants of each kind of atom, to account for the fact that bond distances and angles are not the same in all molecules, differing slightly with the environment.
Of course, a graphical presentation can adapt itself to all of these styles of presentation, according to the degree of refinement which is required at the moment.