Abstract 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 2D 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. The case of defect electron spins (driver / probe) interacting via hyperfine coupling is studied with nuclear spins of H atoms chemisorbed onto (001) and (111) 3C‐SiC surfaces. The system fabrication processes is stimulated with super lattice kinetic Monte Carlo (SlKMC), 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). A rich scenario of metastable spin‐waves is identified in the quantum simulation setting. The interaction between protocols and variable system configurations could hinder the effectiveness of the preparation/measurement phases.