You can try the model-based control design because you already have the model constructed using blocks in the Simulink environment. Sometimes it is difficult to tell what's going on when the Simulink model is displayed partially or with chaotic jumbled connections.
If you provide the full model in mathematical equations (ODEs) with proper descriptions of the symbols and process variables, then people can help identifying the control loop and the location of the control input. With that info, people can guide you accurately where to put the PID controller block.
