Placing the probe on the fermenter and insulating it from the ambient air seems to work best for me. I've tried putting it in free air, a jar of water and against the fermenter.
My main problem with having it in free air was that the freezer cycled on/off every 10-15 minutes. This would lead to considerable excess wear on the compressor. When the probe was in a jar of water the freezer cycled less often, but the actual temperature of the fermentation went higher because of the yeast activity. Placing the probe against the fermenter and insulated from the air compensated for the temperature rise of the fermentation. I did one experiment of placing the probe in a thermowell in the beer, but didn't see any major difference, except for one additional item to sanitize.
It did take quite a bit of experimentation using multiple temperature probes with a BCS-460 to come to my conclusion, but I'm confident that my method works best with my equipment.