On separation: The transceiver modules can be co-located, and antenna separation isn't really a concern. Go for at least 1 foot of separation though.
Two com radios, if anyone following along is in that boat, is a bigger deal. In that case, the modules can be co-located, but you want at least 4 feet of antenna sep; 6 feet or more ideally. It's also ideal to have one antenna on the top of the aircraft, and another on the bottom, as well, if you're using normal externally mounted antennas. In this case, you usually make the primary COM the one facing down.
Two com radios, if anyone following along is in that boat, is a bigger deal. In that case, the modules can be co-located, but you want at least 4 feet of antenna sep; 6 feet or more ideally. It's also ideal to have one antenna on the top of the aircraft, and another on the bottom, as well, if you're using normal externally mounted antennas. In this case, you usually make the primary COM the one facing down.