For a thermostat like a ranco, jc, herpstat, or helix, there's one probe that controls one of the heat sources. Probe placement can be tricky with multiple cages since while it controls the one cage, the other cage without the probe may or may not be at the same temperature as the other, due to variables involved in your particular setup.

The trick is to place the single probe in such a way that both heat sources are where you want them to be.