Care should be taken when installing an ptFlex into a High Altitude Balloon capsule, as several factors can seriously hurt your chances for a successful launch and recovery.
In enclosure itself should be semi-airtight as to not allow excessive amounts of air to pass across the flight controller or the battery. Styrofoam, polyurethane foam (as used in seat cushions) and packing peanuts all make good materials with which to pack around the avionics to keep them fixed in place and out of the breeze.
The ptFlex should be mounted in such a way that there are no other metallic obstructions around the GPS or VHF antennas. Metallic objects can shield the GPS antenna from receiving a positioning signal from the satellites and can detune the antennas from their optimum resonance. Detuned antennas will affect their overall performance, and can make them completely non-functional in worst-case scenarios. It should also be noted that detuned VHF transmitting antennas can cause permanent damage to the transmitter.
Ideally the ptFlex board should be mounted flat, with the component side of the PCB facing towards the open sky. The battery pack should be mounted nearby, with as short of cable as practical. Be aware of any other wires or conductive surfaces that may come in contact with the ptFlex circuit board, and insulate the accordingly. Failure to do could could result in damaged electronics, loss of the tracking system, or even fire.
The VHF transmitting antenna should be mounted in a vertically polarized fashion (typically up and down), and should be several centimeters away from the ptFlex, but connected with as short of coax cable as possible. The VHF antenna is typically mounted onto the outside of flight capsule, but be careful to structurally support the antenna and coax, as the package can sustain significant damage upon landing, especially if it is drug along the ground due to high surface winds.
WARNING: Always thoroughly test the installation of the tracking system in the capsule where it will be mounted, with any and all other equipment installed and turned on. In extreme situations, other nearby devices have been known to cause harmful interference to the sensitive GPS receiving system. Keep in mind that the tracker will probably not land in an upright position, so be sure to test the GPS operation in an open area, and in all possible landing configurations.