We describe methods for capturing and analyzing EHR use and clinical workflow of physicians during outpatient encounters and relating activity to physicians' self-reported workload. We collected temporally-resolved activity data including audio, video, EHR activity, and eye-gaze along with post-visit assessments of workload. These data are then analyzed through a combination of manual content analysis and computational techniques to temporally align streams, providing a range of process measures of EHR usage, clinical workflow, and physician-patient communication. Data was collected from primary care and specialty clinics at the Veterans Administration San Diego Healthcare System and UCSD Health, who use Electronic Health Record (EHR) platforms, CPRS and Epic, respectively. Grouping visit activity by physician, site, specialty, and patient status enables rank-ordering activity factors by their correlation to physicians' subjective work-load as captured by NASA Task Load Index survey. We developed a coding scheme that enabled us to compare timing studies between CPRS and Epic and extract patient and visit complexity profiles. We identified similar patterns of EHR use and navigation at the 2 sites despite differences in functions, user interfaces and consequent coded representations. Both sites displayed similar proportions of EHR function use and navigation, and distribution of visit length, proportion of time physicians attended to EHRs (gaze), and subjective work-load as measured by the task load survey. We found that visit activity was highly variable across individual physicians, and the observed activity metrics ranged widely as correlates to subjective workload. We discuss implications of our study for methodology, clinical workflow and EHR redesign.