I haven't done this, but I agree that it would make the most sense to not use the 990's headphone jack to feed a separate headphone amp. Two options come to mind: use the left/right pre-amp outputs or use the second zone outputs. A third option would be one of the line-level record outputs, assuming that the headphone amp has volume control, but I don't think it's likely to be as good an approach.

I might lean toward the left/right pre-amp outputs if you are presently using the balanced left/right pre-amp outputs for your main system, although there are some control problems that we'll get to in a moment. If you are using the unbalanced pre-amp outputs already, you would need to add a well-made splitter and re-calibrate the system to adjust for the split. One drawback to this scenario is that both the headphone amp and the main amp are going to get the same signal with the same volume control. You'd have to manually turn off the main amp if you wanted to listen to the headphones only. You'd also have to make sure you are using a stereo mode when listening to headphones - don't want the signal being spread across all five or seven speakers when you are only using two of them. As we've said, the 990's volume control would also act on the signal, so if the headphone amp has a volume you'd probably want to find a good spot to set it to.

The second zone would probably be the most convenient thanks to the independent volume control and input selection. The second zone only works with stereo analog sources, though, which means you might have to run additional stereo analog connections to the 990's inputs and shifting the D/A burden from the 990 to those sources for sources that would otherwise be connected digitally. This is the direction that I'd probably lean toward. As with the pre-amp outputs, this approach includes a volume control at the 990.

A third option is to use the Tape or Video1 output to feed the headphone amp. I don't recall at the moment if the record outputs work with digital inputs or not - if they don't, you'd have the same input considerations as you have for the second zone. This approach would not have any volume control at the 990 (not sure what mute would do). It would also be tied to the main pre-amp outputs for input selection. It's probably the least convenient of the three scenarios.