In outpatient healthcare clinics, capacity, patient flow, and scheduling are rarely managed in an integrated fashion, so a question of interest is whether clinic performance can be improved if the policies that guide these decisions are set jointly. Despite the potential importance of this issue, we find surprisingly few studies that look at how the allocation of capacity, paired with various appointment scheduling policies and different patient flow configurations, affects patient flow and clinical efficiency. In this paper, we develop an empirically based discrete-event simulation to examine the interactions between patient appointment policies and capacity allocation policies (i.e., the number of available examination rooms) and how they jointly affect various performance measures, such as resource utilization and patient waiting time. Findings suggest that scheduling lower-variance, shorter appointments earlier in the clinic (and, conversely, higher-variance, longer appointments later) results in less overall patient waiting without reducing physician utilization or increasing clinic duration. Additionally, exam rooms exhibited classic bottleneck behavior: there was no effect on physician utilization by adding exam rooms beyond a certain threshold, but too few exam rooms were devastating to clinic throughput. Some significant interactions between these variables were observed, but were not influential to the level of managerial concern. Clinicians' intuition about managing capacity in healthcare settings may differ substantially from best policies.