Absorbing such a large amount of energy in the form of photons increases the temperature of the lower layers, which then rise up and are replaced by the cooler and denser upper layers. This process is called convection and this forms the mode of transfer of energy across the convection zone. The convection cycles get smaller as we approach the outer layers of the convection zone. The gas atoms then enter the photosphere and re-emit the photons. These photons again travel to us in the radiation mode and reach the Earth.
Sunspots are cooler regions, as compared to the surrounding photosphere.
The magnetic field lines in the Sunspot are about 1000 times stronger than the surrounding region. These strong field lines deviate the energetic charged particles, hence creating cooler regions. The Sun's magnetic field sometimes erupts out of the photosphere in to the corona. The charged particles then follow these loops, and what results is a prominence. A flare is essentially the same phenomena, but it is more violent than a prominence and lasts only for a few minutes, while a prominence lasts for days.