We have developed HiNTS, the Hierarchical Nanoparticle Transport Simulator, and adapted it to study commensuration effects in two classes of Nanoparticle (NP) solids: (1) a bilayer NP solid (BNS) with an energy offset, and (2) a BNS as part of a Field-Effect Transistor (FET). HiNTS integrates the ab initio characterization of single NPs with the phonon-assisted tunneling transition model of the NP-NP transitions into a Kinetic Monte Carlo based simulation of the charge transport in NP solids. First, we studied a BNS with an inter-layer energy offset ∆, possibly caused by a fixed electric field. Our results include the following. (1) In the independent energy-offset model, we observed the emergence of commensuration effects when scanning the electron filling factor F F across integer values. These commensuration effects were profound as they reduced the mobility by several orders of magnitude. We analyzed these commensuration effects in a five dimensional parameter space, as a function of the on-site charging energy EC , energy offset ∆, the disorder D, the electron filling factor F F , and the temperature kBT . We demonstrated the complexity of our model by showing that at integer filling factors F F commensuration effects are present in some regions of the parameter space, while they vanish in other regions, thus defining distinct dynamical phases of the model. We determined the phase boundaries between these dynamical phases.(2) Using these results as a foundation, we shifted our focus to the experimentally much-studied NP-FETs. NP-FETs are also characterized by an inter-layer energy offset ∆, which, in contrast to our first model, is set by the gate voltage VG and thereby related to the electron filling F F . We repeated many of our simulations and again demonstrated the emergence of commensuration effects and distinct dynamical phases in these NP-FETs. Notably, the commensuration effects in the NP-FETs showed many similarities to those in the independent energy-offset BNS.