What we usually understand with ambient temperature is the temperature in the shade - that's the temp the standard weather stations try to report.
For cloud detection, however, we don't need an exact ambient temperature but something that follows that temperature, so the original CloudWatcher units used the IR sensor's internal thermometer to report the ambient temperature. The result was always some degrees above "real" ambient temperature, but that was good enough for our purposes.
Adding the relative humidity sensor (external version), which also includes a temperature one, has allowed us to read a quite good ambient temperature measurement, as this sensor is placed below the unit, thus protected from sunlight, and in a separate (negligible electronics heat), ventilated enclosure.
In the software, there are now several options to select both the source of the ambient temperature and an optional offset.
If using the external RH sensor, the offset should be set at 0:
If using the IR sensor, some value is called for, and the readings will not be so accurate (but, as mentioned, good enough for cloud detection).