Hi All,
I'm the developer of Atomsmith and thought that I'd chime in here.
It's true that the physics of atomic structure is very different from that of planetary motion. In fact, that very fact plays a central role in the history of the development in the theory of the atom, which is basically a 2,000 year exercise in the scientific method. Atomsmith does have tools to "build" atoms from scratch. Users interact with them via the symbolic representation called an "orbital box diagram."
Atomsmith does cost a lot more than the Universe Sandbox -- it's targeted toward schools and has a very expansive curriculum that works with the models. We do have pricing for individuals too, but it's not $19.99.
On the other hand if you have a Mac, you can get much of the functionality for $14.99 in our Atomic Dashboard product, which is available on the Mac App store:
http://www.bitwixt.com/jsite/atomicdashboardIf you go there, have a look at the "A Tour of the Element Carbon" screencast to get an idea of how atoms are built by placing electrons in atomic orbitals (as opposed to the orbits in the solar system).
Have a great day and great job on the Universe Sandbox!