As embedded applications are subject to non-functional requirements (latency, safety, reliability, etc.) they require special care when it comes to providing assurances. Traditionally, these systems are quite static in their software and hardware composition. However, there is an increasing interest in enabling adaptivity and autonomy in embedded systems that cannot be satisfied with preprogrammed adaptations any more. Instead, it requires automated software composition in conjunction with model-based analyses that must adhere to requirements and constraints from various viewpoints. A major challenge in this matter is that embedded systems are subject to emergent constraints which are affected by inter-dependent properties resulting from the software composition and platform configuration. As these properties typically require an in-depth evaluation by complex analyses, a holistic formulation of parameters and their constraints is not applicable. We present a compositional framework for model-based integration of component-based embedded systems. The framework provides a structured approach to perform operations on a cross-layer model for model enrichment, synthesis and analysis. It thereby provides the overarching mechanisms to combine existing models, analyses and reasoning. Furthermore, it automates integration decisions and enables an iterative exploration of feasible system compositions. We demonstrate the applicability of this framework on a case study of a stereo-vision robot that uses a component-based operating system.