Over the last few years, multi-FPGA-based prototyping becomes necessary to test System On Chip designs. However, the most important constraint of the prototyping platform is the interconnection resources limitation between FPGAs. When the number of inter-FPGA signals is greater than the number of physical connections available on the prototyping board, signals are time-multiplexed which decreases the system frequency. We propose in this paper an advanced method to route all the signals with an optimized multiplexing ratio. Signals are grouped then routed using the intra-FPGA routing algorithm: Pathfinder. This algorithm is adapted to deal with the inter-FPGA routing problem. Many scenarios are proposed to obtain the most optimized results in terms of prototyping system frequency. Using this technique, the system frequency is improved by an average of 12.8%.