Once the Controller is connected to a radio module, and the radio module is hooked to it's duplexers and antennas, then you can begin testing of the basic repeater functionality.
Set a radio to the frequency and offset, and make sure that it is set for DV. When you key the radio, no matter what the programming, the repeater should respond with it's callsign and module. Without the repeater information specified in the RPT1 field, the repeater will not repeat your signal, only identify itself.
Once you program the correct RPT1 field in a radio, the repeater should start repeating your signal. There will be a short delay in the audio due to the digital encoding and decoding. If there are any issues, then there's only about 3 areas in which there could be a problem, the radio module's programming, the connection between the module and the controller, and the controller's programming.
Regrettably, there is very few diagnostics in the system. There is no indication that anything is working when looking at the controller, radio modules, or even the software applications. Luckily, there isn't that much that can go wrong and there have been few problems with the connectivity.