The interplay between pairs of critical factors such as performance, energy and reliability within modern computing systems has always been an interesting topic of study. However, studying the interplay of all three factors together in a many-core, multi-layer design setting has been a relatively recent undertaking. This work explores the practical problems encountered in such studies and introduces the modelling framework ArchOn, which is based on a novel resource-driven graph representation. ArchOn facilitates the analysis and potentially design and synthesis of systems whose design domains are more conveniently organized into multiple layers or levels (e.g. application, OS, hardware, etc.) and potentially large scale and diverse types of concurrency. The layer-agnostic formalism helps designers reason about cross-layer issues and the resource-driven approach is advantageous for reasoning about such issues as energy and time. Example single-and multi-core case studies help explain and illustrate the method.