Hi Dpark,
What type of aircraft are you flying?
Lots of people have fitted external antennas to metal bodied aircraft. The best one for P3i transceive is a 1/4 wave monopole, which can be fitted using one of the 3 metre co-ax extension leads - both available from the PilotAwareHardware.com site. This needs a metal ground plane to ensure effective horizontal transmission radiation, so fitting to a metal bodied aircraft is ideal. When fitted, it can be easily weather-sealed by applying a thin smear of silicone under the joint during fitting. Remember, however that you need official approval from your permit authority as drilling holes in your aircraft constitutes a modification.
Because of the much higher transmit power, the 1090MHz receive only antenna normally works fine when located internally - just try to give it as clear a view of 'sky' as possible - e.g. through a window. If you have to fit an external one, I would go for the same type as are sold for transponder use as these are both sturdy and weatherproof.
In all cases, try to keep antennas at least 300mm apart.
Regards
Peter