facilitate both meticulous simulation and streamlined design optimization, we introduce a multi-level simulation framework that spans both Hamiltonian and quantum error correction levels, and is equipped with the capability to compute gradients efficiently. This toolset aids in design optimization, tailored to specific objectives like quantum memory performance. Within our framework, we investigate the often-neglected spatially correlated unitary errors, highlighting their significant impact on logical error rates. We exemplify our approach through the multi-path coupling scheme of fluxonium qubits.