There isn't anything happening on the atomic level that isn't already adequately described by the classical theory. You excite an electromagnetic wave at your source and you do so inside of a waveguide. The waveguide is structured in a way that directs the propagation of the wave along a desired direction. This waveguide feeds into the antenna. The antenna acts as a transition from guided to propagating wave and vice-versa. A lot of times this can be seen as a direct physical process as we describe. For example, we can feed the wave into a resonant chamber that allows radiation to leak out in a desired direction. This can be done by leaving gaps in the chamber. This is roughly how a patch antenna works. The area between the patch and the ground acts as a resonant chamber to trap the energy of the guided wave. But the sides of the chamber are open and thus energy can leak out of the sides (or in in the case of receiving).
A horn antenna works by gradually transitioning a rectangular waveguide into an infinitely open waveguide (ie, free-space). This is done by steadily increasing the size of the waveguide and thus you get a horn. Ideally it would keep increasing to an infinite size but in the interests of reality we have to truncate the horn at some point.
A dipole antenna is a rough realization of a horn antenna. The wave is guided between the two arms of the antenna and then the wires suddenly separate allowing for the guided wave to hit the gap and propagate out. Think of the arcing in a Jacob's Ladder.
The energy isn't carried by the electrons. It is carried by the electromagnetic wave and it is the wave that excites these currents. However, electromagnetic waves and currents are for the most part inseparable. When you have one you have to have the other and thus the lines of causality can be a bit blurred. Take the case of sourcing the electromagnetic waves. Do you do this by exciting an alternating electric field which creates an electromagnetic wave that then induces the currents in the waveguide? Or do you excite the currents in the waveguide which create the electromagnetic wave? I do not think that this is really that ambiguous. Technically we do not really have many (if even) means of exciting currents without first inducing an electric field to direct the currents in the manner that we wish. Still, it can become confusing sometimes. In the case of antennas and waveguides, the actual source currents are back at the generator of the electromagnetic wave. All the other currents along the waveguide and on the antenna and so forth are induced by the resulting electromagnetic waves since the source currents and voltages are localized.
Now in terms of photons, the photon is simply the carrier of the energy of the electromagnetic wave. So the amplitude and direction of propagation of the wave is indicative of the density and direction of movement of the photons that make up the wave.