Ubiquitous computing and communication environments connect systems and people in unprecedented ways, but also fundamentally challenge the mindset of traditional systems engineering. Complex techno-social systems exhibit spontaneous self-organization properties, based on decentralized interactions among a multitude of agents, that have preceded our ability as human designers to fully comprehend and control them. This should prompt us to steer away from managing details and, instead, focus on establishing the generic conditions for systems to develop and evolve under our guidance. In alignment with this paradigm shift we propose a methodological framework termed emergent engineering for deploying large-scale "eNetwork" systems, and illustrate it with self-organized security (SOS) scenarios. It involves an abstract model of programmable network self-construction in which nodes execute the same code, yet differentiate according to position. We illustrate these principles on a future application to SOS pointing to how this could lead to a new type of controllable self-organization, able to dynamically co-evolve the system with its environment.