I would definetly use a whip on one of the antennas assuming that you use 35 mhz.

72 mhz have better range from what I'm told.
Heared a story about the JWM in UK some years ago when the Americans had to put 35 mhz receivers in their planes and still kept the antenna inside the plane as I understand is normal in the US.
The story said there was a lot of range/ interference issues.

That being said, on the two flights I had with the Lightning/ Weatronic this weekend, none of areials was ever low on signal at any point during the flights. One of them is located inside the fuse while the other is on a whip....

What I saw was that when one of the antennas had a lower signal, the other one was usually stronger at the same time. It still kept antenna 1 as "used" at all times during the flights as the signal was alway good enough.