Magnetic monopoles in frustrated magnets are paradigmatic fractionalised quasiparticles, yet no experimental platform simultaneously tunes their confinement and preserves ice-rule physics. Here we exploit the native bilayer architecture of a D-Wave Advantage2 quantum annealer to realise the first programmable two-plane kagome spin ice, spanning 1,536 logical spins across a 4×13×14 grid of system size, interlayer coupling, and quantum drive. We find that interlayer exchange drives a sharp transition from ferroelectric to antiferroelectric staggered charge order, an Ice-II phase with no classical or single-layer analogue, with a critical onset at (J_⊥/J₁)^* ≈ 0.044 that is stable across five decades of annealing time. Restricting the charge structure factor to ice-rule plaquettes reveals an order-of-magnitude enhancement over conventional all-plaquette estimators, demonstrating that quantum-selected charge order is invisible to defect-diluted probes and establishing a methodological standard for future quantum spin ice experiments. The quantum renormalisation of the monopole chemical potential sets a concrete engineering target for the transmon circuit-QED kagome ice required to enter the monopole deconfinement regime. Three falsifiable predictions follow for existing Ni₈₁Fe₁₉ nanowire bilayer architectures: a critical interlayer separation, an elevated monopole activation temperature, and an order-of-magnitude enhancement of the Ice-II signal in published X-ray datasets, all testable without new fabrication.