Intrusion detection for network security is a computation intensive application demanding high system performance. System level design, a relatively unexplored field in this area, allows more efficient communication and extensive reuse of hardware components for dramatic increases in area-time performance. By applying optimization strategies to the entire database, we reduce hardware requirements compared to architectures designed with single pattern matchers in mind. We present a methodology for system-wide integration of graph-based partitioning of large intrusion detection pattern databases. Integrating ruleset-based graph creation and min-cut partitioning, our methodology allows efficient multi-byte comparisons and partial matches for high performance FPGA-based network security. Through pre-processing, this methodology yields designs with competitive clock frequencies that are a minimum of 8x more area efficient than previous non-predecoded shift-and-compare architectures.