Re atomic transitions: you can nicely describe the complete transition from beginning orbital to final orbital with emission (or absorbtion) of a photon by means of standard time-dependent QM. This was discussed, in a ground-breaking paper, by Wigner and Weisskopf in the 1920s or 1930's, and is a topic widely discussed in the research literature and textbooks. I'll recommend the books on QED by Cohen-Tannoudji, Dupont-Roc and Grynberg, in which the issue of atomic transitions involving photons are described in extraordinary detail. Everything you want to know is there -- some of it is not easy. You pose a problem that's been well understood for close to a century, and is, in fact, central to much of field theory and particle physics.
Other names that are relevant are scattering theory, resonance production and decay, nuclear transitions.
Within the spirit of QM theory, you can always find the electron, before, during or after the transition -- well sort of --. The key, in this regard, is the typical time integral that gives the ubiquitous 'finite delta function",
sin(dE*t)/dE, where dE is the energy difference between the final and initial states. As long as the "time length of the experiment, t, is finite, then the electron can be in either the initial or final state, as in a superposition. We are getting farther into S matrices and scattering theory than I anticipated.
There's, as I said earlier, a huge literature on this subject -- do a Google on Wigner-Weisskopf, Breit-Wigner, resonances, resonant scattering, line breadth, radiative reactions, scattering theory, atomic and nuclear radiation, quantum optics, ...
How does the transition happen? With absorbtion, the energy of the electron changes, and thus changes must occur in the wave function -- usually described by means of time-dependent perturbation theory -- due to the governance by the systems' Schrodinger equation. Given the right tools, QM does a very nice job of describing the evolution of an atomic transition in a blow-by-blow fashion. That is, the Schrodinger Eq gives a complete account of the evolution of the wave function, and hence of the probabilities governing possible experiments.
Regards,
Reilly Atkinson