As the level of analysis grows from the individual, to the team or group, to the organization, the research methods applied used to evolve to address the uncertainties brought on by scope. Software organizations provide a scenario that blends intensive knowledge work with extremely high velocities. The nature of the problem being studied, significantly drives the choice of a variance research design or a process research design. The focus on enterprise agility in software organizations is more conducive to a process research design, and the study is theory generating in nature, we adopt a combination of grounded theoretic methods and comparative case analysis. In this paper, we share the research approach developed, and provide examples of how the study was designed, the data collected, reduced and analyzed. We conclude with a set of lessons learned that are applicable for engaging and collaborating with software organizations.