In a multiple flowline manufacturing system, such as a typical printed circuit board (PCB) production system, scheduling tasks include determining due dates of customer orders, assigning products to daily production, and releasing boards to production lines each day. The main challenge for the scheduling system is to coordinate different production resources so they can work together to improve system performance. The Bi-Level Intelligent Scheduling System (BLISS) was developed, using a two-level scheduling approach integrating product-level and board-level scheduling, to schedule jobs for PCB manufacturing systems under a daily through weekly planning horizon. A utility function is added to determine lot size, and four sequencing rules are evaluated to find the most suitable rule for the scheduling schemes under study. The lot sizing and sequencing decisions are integrated with the simulation module to generate more accurate schedules, with special emphasis put on the need for coordination. Performance of the two-level scheduling approach is evaluated and compared with that of using product-level or board-level scheduling alone under a variety of manufacturing scenarios. The performance is analyzed under various environments such as different degrees of due date tightness, order variation, and product variation. Results show the strength of the two-level scheduling approach, especially in “mission-critical” situations of tight due dates, high variation of orders, and highly changeable products. The findings also provide guidelines for applying those scheduling schemes effectively and efficiently.