Layering two-dimensional van der Waals materials provides unprecedented control over atomic placement, which could enable tailoring of vibrational spectra and heat flow at the sub-nanometer scale. Here, using spatially-resolved ultrafast thermoreflectance and spectroscopy, we uncover the design rules governing cross-plane heat transport in superlattices assembled from monolayers of graphene (G) and MoS2 (M). Using a combinatorial experimental approach, we probe nine different stacking sequences: G, GG, MG, GGG, GMG, GGMG, GMGG, GMMG, GMGMG and identify the effects of vibrational mismatch, interlayer adhesion, and junction asymmetry on thermal transport. Pure G sequences display signatures of quasi-ballistic transport, whereas adding even a single M layer strongly disrupts heat conduction. The experimental data are described well by molecular dynamics simulations which include thermal expansion, accounting for the effect of finite temperature on the interlayer spacing. The simulations show that a change of only 1.5% in the layer separation can lead to a nearly 100% increase of the thermal resistance. Using these design rules, we experimentally demonstrate a 5-layer GMGMG superlattice with an ultralow effective cross-plane thermal conductivity comparable to air, paving the way for a new class of thermal metamaterials with extreme properties.