What you seem to be describing as a roofing system is an IRMA (Inverted roof membrane assembly). With a non permeable roof insulation, you will see very little variation in temperature other than heavy ballast and residual moisture within the concrete over the insulation. The purpose of your inspection is to determine the openings within the roof membrane leading to water leakage to the building interior. Sadly you will not be able to detect these leaks with infrared thermography from the exterior.
The best method of detection of membrane defects within IRMA roofs is by a technology called EFVM (Electro Field Vector Mapping). This technology employs placement of low voltage wiring around the perimeter of the entire roof area along with isolation wiring around all pentrations in the roof assembly. By flooding the roof assembly and inducing a low voltage through the perimeter wiring, electrical prods are used on the surface materials to locate leaks by analysis of reading of directional signals from the prods.
All other NDT methods to detect roof membrane defects cannot compete with EFVM in terms of accuracy and cost. Thermography is not applicable on this type of roof assembly.