In System Generator, you can use cross probing between the signal in the Xilinx Waveform Viewer and the Simulink® diagram to aid the debugging process.
To add a signal to the Waveform viewer, right-click the signal in the model and select Xilinx Add To Viewer. Simulating the design should launch the Waveform Viewer as shown below.
All signals in same clock domain are colored similarly. In the
figure above: src_domain/Slice/Out1
and
dest_domain/Relational/Out1
are in
different clock domains.