In recent years, the expectations for high throughput satellite (HTS) have diversified based on rapid increase in traffic demands. However, the Ku-band and Ka-band utilized by HTS are growing tighter. It is necessary to utilize the limited frequency ranges efficiently and share resources with other communication systems. The digital beam forming (DBF), which has a high area flexibility for allocating power resources, is being developed to adapt to the diversification of communication applications. However, it remains unclear how multi-spot beam placement is related to throughput in an HTS communication system equipped with DBF. In this study, we attempted to determine how the distances between spot beams in the same frequency band and the distances between adjacent spot beams in different frequency bands are related to overall system throughput and to derive a multi-spot beam arrangement to improve overall system throughput. The main contributions of this study are the clarification of relationships between the positions of multi-spot beams and overall system throughput and the construction of a novel mathematical model to derive multi-spot beam arrangements to enhance overall throughput. The effectiveness of our proposal is evaluated through numerical analysis.