We present and analyze deep Herschel/HIFI observations of the [CII] 158um, [CI] 609um, and [CI] 370um lines towards 54 lines-of-sight (LOS) in the Large and Small Magellanic clouds. These observations are used to determine the physical conditions of the line--emitting gas, which we use to study the transition from atomic to molecular gas and from C^+ to C^0 to CO in their low metallicity environments. We trace gas with molecular fractions in the range 0.1<f(H2)<1, between those in the diffuse H2 gas detected by UV absorption (f(H2)<0.2) and well shielded regions in which hydrogen is essentially completely molecular. The C^0 and CO column densities are only measurable in regions with molecular fractions f(H2)>0.45 in both the LMC and SMC. Ionized carbon is the dominant gas-phase form of this element that is associated with molecular gas, with C^0 and CO representing a small fraction, implying that most (89% in the LMC and 77% in the SMC) of the molecular gas in our sample is CO-dark H2. The mean X_CO conversion factors in our LMC and SMC sample are larger than the value typically found in the Milky Way. When applying a correction based on the filling factor of the CO emission, we find that the values of X_CO in the LMC and SMC are closer to that in the Milky Way. The observed [CII] intensity in our sample represents about 1% of the total far-infrared intensity from the LOSs observed in both Magellanic Clouds.
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