This paper studies the real-life problems of outpatient clinics having the multiple objectives of minimizing resource overtime, patient waiting time, and waiting area congestion. In the clinic, there are several patient classes, each of which follows different treatment procedure flow paths through a multiphase and multiserver queuing system with scarce staff and limited space. We incorporate the stochastic factors for the probabilities of the patients being diverted into different flow paths, patient punctuality, arrival times, procedure duration, and the number of accompanied visitors. We present a novel two-stage simulation-based heuristic algorithm to assess various tactical and operational decisions for optimizing the multiple objectives. In stage I, we search for a resource allocation plan, and in stage II, we determine a block appointment schedule by patient class and a service discipline for the daily operational level. We also explore the effects of the separate strategies and their integration to identify the best possible combination. The computational experiments are designed on the basis of data from a study of an ophthalmology clinic in a public hospital. Results show that our approach significantly mitigates the undesirable outcomes by integrating the strategies and increasing the resource flexibility at the bottleneck procedures without adding resources.