The full design of relevant systems for quantum applications, ranging from quantum simulation to sensing, is presented using a combination of atomistic methods. A prototypical system features a two-dimensional ordered distribution of spins interacting with out-of-plane spin drivers/probes. It could be realized in wide-bandgap semiconductors through open-volume point defects and functionalized surfaces with low Miller indexes. We study the case of defect electron spins (driver / probe) interacting via hyperfine coupling with nuclear spins of H atoms chemisorbed onto \hkl(001) and \hkl(111) 3C-SiC surfaces. We simulate the system fabrication processes with super lattice kinetic Monte Carlo, demonstrating that epitaxial growth under time-dependent conditions is a viable method for achieving controlled abundance or depletion of near-surface point defects. Quantum features are evaluated by means of extensive numerical analysis at a full quantum mechanical level based on calibrated models of interacting spin systems. This analysis includes both stationary (relative stability of ordered states) and time-dependent (protocols) conditions, achieved varying the model parameters (in our case the atomic structure and the external field). We identify a rich scenario of metastable spin-waves in the quantum simulation setting. The interaction between protocols and variable system configurations could hinder the effectiveness of the preparation/measurement phases.