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Noisy Intermediate-Scale Quantum Computing (NISQ) has dominated headlines in recent years, with the longer-term vision of Fault-Tolerant Quantum Computation (FTQC) offering significant potential albeit at currently intractable resource costs and quantum error correction (QEC) overheads. For problems of interest, FTQC will require millions of physical qubits with long coherence times, high-fidelity gates, and compact sizes to surpass classical systems. Just as heterogeneous specialization has offered scaling benefits in classical computing, it is likewise gaining interest in FTQC. However, systematic use of heterogeneity in either hardware or software elements of FTQC systems remains a serious challenge due to the vast design space and variable physical constraints. This paper meets the challenge of making heterogeneous FTQC design practical by introducing HetArch, a toolbox for designing heterogeneous quantum systems, and using it to explore heterogeneous design scenarios. Using a hierarchical approach, we successively break quantum algorithms into smaller operations (akin to classical application kernels), thus greatly simplifying the design space and resulting tradeoffs. Specializing to superconducting systems, we then design optimized heterogeneous hardware composed of varied superconducting devices, abstracting physical constraints into design rules that enable devices to be assembled into standard cells optimized for specific operations. Finally, we provide a heterogeneous design space exploration framework which reduces the simulation burden by a factor of 104 or more and allows us to characterize optimal design points. We use these techniques to design superconducting quantum modules for entanglement distillation, error correction, and code teleportation, reducing error rates by 2.6 ×, 10.7 ×, and 3.0 × compared to homogeneous systems.