Embedding research and evaluation into organizations is one way to generate "practice-based" evidence needed to accelerate implementation of evidence-based innovations within learning health systems. Organizations and researchers/evaluators vary greatly in how they structure and operationalize these collaborations. One key aspect is the degree of embeddedness: from low embeddedness where researchers/evaluators are located outside organizations (eg, outside evaluation consultants) to high embeddedness where researchers/evaluators are employed by organizations and thus more deeply involved in program evolution and operations. Pros and cons related to the degree of embeddedness (low vs high) must be balanced when developing these relationships. We reflect on this process within the context of an embedded, mixed-methods evaluation of the Veterans Health Administration (VHA) Diffusion of Excellence (DoE) program. Considerations that must be balanced include: (a) low vs high alignment of goals; (b) low vs high involvement in strategic planning; (c) observing what is happening vs being integrally involved with programmatic activities; (d) reporting findings at the project's end vs providing iterative findings and recommendations that contribute to program evolution; and (e) adhering to predetermined aims vs adapting aims in response to evolving partner needs.