Rick's post starts to sort things out, but before you get too far into frustration, I'd need to ask a few more questions.
1) Which "appropriate Tru Trak Autopilot"? just about any of their systems will work with the GRT stuff, and it can be a very simple heading-hold/Nav Trak using Serial data or a full-up VSGS with ARINC and GPSS. How you operate it will depend on which autopilot.
2) Is there an internal GPS as well? How are the GPS's configured? Is the 396 connected to GPS 1 or GPS 2 in software, and are the serial ports properly configured?
3) Is the setup within the HX correct? These things are very "configurable" - which gives you a lot of capability, but also a lot of ways to not get them set up properly. I have helped a lot of people set up their aircraft with GRT equipment, and so far, have never met two identical configurations.
Until we know how the hardware is connected in that particular aircraft, and then how it is configured, everything else is a guess. It doesn't take long to get set up once we know that - but until then, it's almost impossible to predict how it will work.
Paul