The [CII] fine-structure transition at 158 micron is frequently the brightest far-infrared line in galaxies. Due to its low ionization potential, C+ can trace the ionized, atomic, and molecular phases of the ISM. We present velocity resolved [CII] and [NII] pointed observations from SOFIA/GREAT on ~500 pc scales in the nearby galaxies M101 and NGC 6946 and investigate the multi-phase origin of [CII] emission over a range of environments. We show that ionized gas makes a negligible contribution to the [CII] emission in these positions using [NII] observations. We spectrally decompose the [CII] emission into components associated with the molecular and atomic phases using existing CO(2-1) and HI data and show that a peak signal-to-noise ratio of 10-15 is necessary for a reliable decomposition. In general, we find that in our pointings greater than or equal to 50% of the [CII] emission arises from the atomic phase, with no strong dependence on star formation rate, metallicity, or galactocentric radius. We do find a difference between pointings in these two galaxies, where locations in NGC 6946 tend to have larger fractions of [CII] emission associated with the molecular phase than in M101. We also find a weak but consistent trend for fainter [CII] emission to exhibit a larger contribution from the atomic medium. We compute the thermal pressure of the cold neutral medium through the [CII] cooling function and find log(P_th/k)=3.8-4.6 [K cm^-3], a value slightly higher than similar determinations, likely because our observations are biased towards star-forming regions.
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