Packaging microelectromechanical systems (MEMS) often accounts for 80 percent of both the cost and the failures of the devices. For biological MEMS with microfluidic channels, packaging requires reliable fluid and electrical connections. This work describes various strategies for optimizing the fabrication of microfluidic circuits and the design of leak-tight, re-usable, multi-functional packaging systems. Various materials are surveyed to determine the appropriate microfluidic chip substrate for an all-polymer device. Three unique test site designs allow combinatorial experiments and improve the functionality of three proven leak-tight packaging fixtures. Finally, the successful deposition of chitosan, a polysaccharide biopolymer that can act as the interface layer between inorganic electrodes and biological components such as proteins and nucleic acids, is shown in a packaged microfluidic environment for the first time. This study lays the groundwork for future applications in miniaturized bio-reactors and chemical and biological sensors.