The first step is to run the A/C system for a few minutes to let it stabilize. Then both probes should be connected side by side at both points that will be temperature tested in the system. For example, if you were testing the temperature drop across the condenser, this would need to be done on both the discharge line and the liquid line.
The contact type units do indeed have a high degree of accuracy, but precautions must be taken when using them (especially connecting to lines) to ensure the accuracy. Otherwise, it is possible to get readings that are easily 5° to 10° off and that can lead to an incorrect diagnosis.
Temperature readings can be easily used to determine if an orifice tube system might be undercharged, and they can also be used to charge an orifice tube system. But if the readings are not accurate, all they are going to do is cause you problems.
Using a contact thermometer, they quickly discovered 50° on the suction line at the expansion valve, and down at the compressor it read 96°. Along any length of hose or tube, there should be very little change in temperature.
