Then you'd create a program that creates variations of the design (called specimens) that vary the design parameters, for example, changing the configuration of a single pin.
A lot of this program is TCL that runs inside Vivado to change the design parameters, because it is a bit faster to load in one Verilog model and use TCL to replicate it with varying inputs instead of having different models and loading them individually.
By looking at all the resulting specimens, you can correlate which bits in which frame correspond to a particular choice in the design.
Looking at the implemented design in Vivado with "Show Routing Resources" turned on is quite helpful in understanding what all choices exist.