Where are the communications antennas normally located on general aviation aircraft?
Honestly? That AOPA article overstates the issue of airframe shadowing (at least for light GA singles): Both antennas will usually work fine on the ground, and will probably work without any issues in the air as well.  

Airframe shadowing can cause issues, but if it were as big an issue as people like to make of it there would be no aircraft with single-radio installations (because they would either not be able to talk to people on the ground, or not be able to talk to people in the air).
There are plenty of aircraft flying around with only one radio.

If you're concerned about whether your transmissions are readable pick a nice quiet time of the day and ask the tower for a radio check on Com #1, then repeat the process on Com #2. (Because we're talking about AM radio the results of this test are valid for your aircraft's position and heading when you did the test, and in weather conditions similar to those the test was conducted.)



The general rule of thumb is that each radio will be connected to a separate antenna (this is necessary if you want them to work independently). Some avionics shops have a preference of which way they wire things, and I'm sure manufacturers have a standard they use in their shops (either the POH or the maintenance manual for your aircraft MAY tell you what the manufacturer's standard is; it may also be noted on the FAA Form 337 for the avionics installation if one was filed).

I've seen varying combinations of which radio is connected to which antenna ("Single radio - Antenna on top" ; "Single radio - Antenna on bottom" ; "#1 Left Wing, #2 Right Wing" ; "#1 Top-Front, #2 Top-Rear", "#1 Top/Ground, #2 Bottom/Air" ; "#1 Bottom/Air, #2 Top/Ground").