We present ForSyDe-Atom, a formal framework intended as an entry point for disciplined design of complex cyber-physical systems. This framework provides a set of rules for combining several domain-specific languages as structured, enclosing layers to orthogonalize the many aspects of system behavior, yet study their interaction in tandem. We define four layers: one for capturing timed interactions in heterogeneous systems, one for structured parallelism, one for modeling uncertainty, and one for describing component properties. This framework enables a systematic exploitation of design properties in a design flow by facilitating the stepwise projection of certain layers of interest, the isolated analysis and refinement on projections, and the seamless reconstruction of a system model by virtue of orthogonalization. We demonstrate the capabilities of this approach by providing a compact yet expressive model of an active electronically scanned array antenna and signal processing chain, simulate it, validate its conformity with the design specifications, refine it, synthesize a sub-system to VHDL and sequential code, and co-simulate the generated artifacts.