Physics education research, electronic materials, and the musings of Christopher Moore, Ph.D.

The degree of detail you use for your model depends on the scale of the system you're interested in.  If you're trying to model the electronic or chemical properties of atoms, you can treat the electrons as quantum particles (with wavefunctions) and treat the proton as a point charge.  If you are interested in nuclear dynamics, then you can introduce a protonic wave function as well that moves in the potential due to the strong force that binds it.  Presumably, in an even higher energy scale, you would introduce quark wave functions, which have even more internal degrees of freedom (i.e., color charge) than do "ordinary" quantum systems.