I don't know enough about high-end headphone amps to speak to the different ways to connect one (headphone jack output vs. stereo analog outputs). I can say that I'm 99.5% certain that there's no way to get access to the Dolby Headphone processing without using the headphone jack. Dolby Headphone is only engaged when the headphone jack is active, which in turn disables the pre-amp outputs. I've never tested the Video1 or Tape record outputs to see if they are still active when in this mode - if they were and the input was digital, I guess there's a chance that they would be getting that Dolby Headphone stereo output, but that goes back to my 99.5% comment since I'm pretty sure that both of those don't happen together.

The 990 has four stereo analog outputs: Video1 record output, tape record output, aux record output, and the second zone. The first three are fixed level outputs (no volume control) while the second zone has its own volume control and input control. If I remember correctly, the 990 will convert digital inputs to stereo analog for the record outputs, but the second zone is essentially a stereo analog pre-amp tucked inside the 990. As such, to use the second zone you need to connect any sources that you plan to listen to through it via analog stereo cables even if you are using digital normally.