How to leverage Lynx NGT-9000's integrated GPS/WAAS?
Sorry, but windmills approach certified GPS systems do not work that way: A GPS approved for IFR navigation and approaches, like a Garmin 430W or GTN650 or an Avidyne IFD440, are more than just an approved position source such as what's included in the NGT-9000 transponder. They have an approved navigation database and interface with (or provide the equivalent of) a Course Deviation Indicator (CDI). 

You can't just suck position data out of the NGT-9000 and fly around using it because while that device has an approved high-quality position source it doesn't have an IFR-approved navigation database, so there's no way to take that GPS data (your position as a point in space) and relate it to known waypoints (VORs, NDBs, airports, intersections, etc.) in a way the FAA considers satisfactory as a primary means of navigation.

You can take the GPS data from it and interface it with an iPad - Foreflight speaks the Lynx L3 language - to use for enhanced situational awareness, which is a huge win, but that's not enough to get you to file GPS flight plans: You would be limited to filing flight plans based on your other installed primary navigation instruments (VOR, ADF, DME).