We use the results of the theory of wave propagation in turbulence to analyze the effects of the atmospheric turbulence on the Free-Space Optical Communication systems under weak and strong scintillation conditions. We found that for the traditional fiber coupling arrangement statistics of the Power-in-Fiber (PIF) is sensitive to the phase fluctuation at the collecting aperture, rather than amplitude fluctuation (scintillation). Larger receiving aperture produces stronger PIF fluctuation. Similar to the scintillation of the sharp focused beams second-order scattering dominates PIF fluctuation for the weak and strong scintillation conditions. This should have serious effect on the probability distribution of the PIF.A new coupling arrangement is suggested that alleviates the destructive effect of the phase fluctuation, and allows the use of large receiving apertures. The trade-off is the decreased coupling efficiency. For our new coupling scheme the PIF fluctuation is determined by the power flux fluctuation through the collecting aperture. This allows taking advantage of the scintillation averaging effect to suppress the fading. We review the results of the rigorous Markov-approximationbased theory of the scintillation averaging that is valid both for a weak and strong scintillation conditions. This technique reveals several distinct regimes of the power flux fluctuation including the situation where fluctuation is relatively small, but is not described by the perturbation (Rytov's) theory. We also show how the energy conservation principle inherent to the wave propagation in the clear air turbulence provides an accelerated rate of the scintillation averaging compare to the typical averaging estimates.