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We present the analysis of Infrared Space Observatory long-wavelength spectrometer (LWS) observations of the two nearby late-type galaxies NGC 1313 and NGC 6946. Both galaxies have been fully mapped in the [C II] far-infrared fine-structure line at 158 µm, and some regions have been observed also in the [O I] 63 µm and [N II] 122 µm lines. We use these observations to derive the physical properties of the atomic interstellar medium, to establish how they relate to other interstellar medium components (gas and dust), and to establish how they vary with different galaxy components such as nucleus, spiral arms, and disk. The [C II] line is the main cooling line of the atomic medium. In NGC 6946 and NGC 1313, its emission represents 0.8% of the infrared emission. Moreover, the [C II] emission can be spatially associated with three components: the nucleus, the star-forming regions in spiral arms, and the diffuse galaxy disk. This last component contributes ≲40% in NGC 6946 and ∼30% in NGC 1313 to the total emission. We apply the photodissociation region (PDR) model by Kaufman et al. to derive PDR physical parameters responsible for the neutral atomic gas emission (G₀, n, and T_s). The results do not significantly differ from what Malhotra et al. recently found by modeling the integrated emission of a sample of 60 normal galaxies. This suggests that the emission in each region under the LWS beam in NGC 6946 and NGC 1313 (corresponding to a linear size of ∼1.5 kpc) is likely to arise from a mixture of components similar to the mixture producing the integrated emission of normal galaxies. However, some regions in NGC 6946 have a G₀/n ratio ∼2-3 times smaller than the mean value found for the normal galaxy sample (1.3), suggesting that the beam-averaged contribution of a less active component in these regions is higher than its contribution in the integrated emission of normal galaxies or, conversely, that the bulk of the integrated emission of the normal galaxies is dominated by a few active regions probably located in their nuclei. CO(1-0) and [C II] in NGC 6946 are well correlated, and the mean [C II]/CO ratio agrees with the mean integrated ratios of the normal galaxies sample. This value (∼500) is a factor of ∼2 less than the mean ratio found for a sample of normal galaxies observed with the Kupier Airborne Observatory (KAO) by Stacey et al. This difference is probably due to the fact that the KAO beam (55") is smaller than the LWS beam (75"), such that the Stacey et al. KAO observations are likely to be more biased toward the nucleus of the galaxies and therefore toward more active regions. In NGC 1313 only four LWS regions have been observed in CO(1-0), and three of them were detected. The [C II]/CO(1-0) seems to systematically increase from the northeast to the south, along the S-shaped spiral arm, indicating that the interstellar medium conditions in NGC 1313 are much more inhomogeneous than the conditions in NGC 6946. H I and [C II] in NGC 6946 are completely uncorrelated, probably because they arise from different gas components: [C II] arises principally in dense and warm PDR and H I from diffuse (n≲3x10³ cm^–3) gas. On the other hand, in NGC 1313 we successfully detect two distinct gas components: a cirrus-like component, for which H I and [C II] are weakly correlated as observed in our Galaxy, and a component associated with dense PDRs completely uncorrelated from H I as observed in NGC 6946. Finally, we find that the H I residing in dense gas surrounding the star-forming regions and presumably recently photodissociated constitutes a few percent of the total H I. In turn, this dense gas component produces most of the [C II] emission emitted by the atomic neutral medium, even if its contribution is lower in NGC 1313 than in NGC 6946. On the other hand, the [C II] emission arising from ionized gas is higher in NGC 1313 than in NGC 6946.