ctcon,
The NPARC website, as far as I know, is still the link you posted; the name of the code may have changed recently (it used to be called NPARC and was a density-based code, the new code called "Wind" is a pressure-based code very similar to Fluent), but the NPARC alliance is still working.
In any case, the user manual for the new code is a free download, and walks you through some simple examples of analysis, as well as discussing the various types of b.c.'s and how they are numerically evaluated or approximated. As mentioned above, there are a lot of papers written to AIAA conferences using the NPARC & Wind codes as the solver. A little research and legwork should get you a ways down the road. You should be able to apply what you've learned from the public documents how to use your in-house code to model similar flows. Or, to learn whether or not the Fluent solver is capable of doing it.
I'm not sure how well the pressure-solver codes (Wind, Fluent) work for transonic or mixed super-/subsonic flow, as I mentioned, the earlier NPARC code was a density-based code that was very robust in mixed super/subsonic flows.