When using instantiation, manually add debug cores, and connect them to signals you want to probe. In the following block design, Debug Hub IP (green) was added and connects to the NoC. Multiple ILA (red) and VIO (purple) cores were added to monitor two counter IP. Green bug icons were added to the signals to be probed by the ILA cores. By explicitly adding the ILA cores and adding probe points, you can define all the debug details early in the design flow.
Figure 1. Instantiation Example