Despite the high sensitivity reached by Photon Detectors so far, the implementation of a background managing system often enforces the robustness of measurements thus creating a resourceful apparatus for specific applications. In this document, the management tools offered by Software Defined Hardware (SDHs) is put to test. By associating the power of FPGAs and Photon Detectors, enhanced measurement stations were assembled. Two different applications, a Bell State Projection Analysis Station and a Photon Counting Optical Time Domain Reflectometry (v-OTDR)Automatic Setup, are presented. Even though both experiments involve the detection of single photons, the background technologies differ drastically.