We present cosmological, radiation-hydrodynamics simulations of galaxy formation during the epoch of reionization in an effort towards modelling the interstellar medium (ISM) and interpreting ALMA observations. Simulations with and without stellar radiation are compared at large (Mpc), intermediate (tens of kpc), and small (sub kpc) scales. At large scales, the dense regions around galaxies reionize first before UV photons penetrate the voids; however, considerable amounts of neutral gas remain present within the haloes. The spatial distribution of neutral gas is highly dynamic and is anti-correlated with the presence of stars older than a few Myrs. For our specific feedback implementation, most of the metals remain inside the virial radii of haloes and they are proportionally distributed over the ionized and neutral medium by mass. For our most massive galaxy with ${\rm M_h}\sim10^{11}$M$_{\odot}$, the majority of the CII and OI mass are associated with cold neutral clumps. NII is more diffuse and arises in warmer gas while OIII arises in hotter gas with a higher ionization parameter, produced by photo-heating and supernovae. If smaller pockets of high metallicity gas exist in the ISM, the emission from these ions may be observable by ALMA while the low metallicity of the galaxy may cause these systems to fall below the local [CII]-SFR relation. The presence of dust can cause spatial offsets between UV/Ly$��$ and [CII] emission as suggested by the recent observations of Maiolino et al. [OIII] may be spatially offset from both of these components since it arises from a different part of density-temperature phase-space.

34 Pages, 26 figures, MNRAS Accepted