This paper details the investigation into the design and control of merging bottlenecks of conveyor-based baggage handling systems, encompassing the merging control algorithm and the impact of the merge's physical layout. A methodology for the analysis of simulation model results is presented. Results show that the layout of the merge influences bag throughput and when the physical configuration is in a preferred position, input variance has no effect on bag throughput performance. These results have potential application to other material handling systems, such as those used in manufacturing and warehousing.