This chapter describes a line of research that seeks to incorporate first-person subjective input into the analysis of meditation-related brain activity and connectivity, as a way to better define and understand everyday mental functions. I present a basic model of naturalistic cognitive fluctuations between mind wandering and attentional states derived from the practice of focused attention meditation. This model proposes four phases in a cognitive cycle: mind wandering, awareness of mind wandering, shifting of attention, and sustained attention. We developed a paradigm to leverage the common experience of awareness of mind wandering during this style of meditation, using subjective reports to drive the analysis of brain imaging data. Results revealed activity in specific brain networks associated with each cognitive phase. Further, participants with more meditation experience exhibited altered patterns of neural activity and resting state functional connectivity compared to participants with less experience. These neural patterns may be involved in the development of cognitive skills such as maintaining attention and disengaging from distraction that are often reported with meditation practice, and suggest mechanisms for how benefits may transfer "off the cushion." Implications for neurophenomenological investigations are discussed, as well as future directions and possible extensions of the model.