Both descriptions are correct and refer to different levels of description. The first one considers the interaction of a classical electromagnetic field with quantized atoms (i.e., a nucleus surrounded by electrons, where the nucleus often is entering the description just through its static electromagnetic field only). This is an approximation, but you get amazingly far with it. E.g., contrary to many textbooks the photoeffect as well as the Compton effect can be described in this socalled "semiclassical approximation".
The second description refers to the fully quantized theory, quantum electrodynamics, i.e., all physical objects, i.e., the electrons, atomic nucleus, and the electromagnetic field. This is the hitherto most comprehensive description, valid for everything observed on atoms today.
The most simple reason, why one needs to quantize the electromagnetic field is spontaneous emission. This describes the fact that if you have a single atom with no other electromagnetic field than that of the nucleus and the electrons (i.e., no em. waves present) and the atom is not in its ground state, sooner or later the atom relaxes to lower states and finally to the ground state emitting one or more photons spontaneously.