To use the second zone (which is a good method of feeding audio to your headphone amp), you will need to provide a stereo analog input to the 990. This could be done by connecting the left/right analog output of the 981HD to any free input on the 990 (either the DVD input that you are probably using anyway or some other input). If you use the DVD input and have that input configured to use a digital input, the second zone will still use the analog stereo input because that's the only one it has access to. And since all outputs of the 981HD are active simultaneously, this should work fine.

Using the pre-amp outputs will sort of negate the value of the headphones: you will be using the same source for both headphones and speakers, and you will be sharing a volume control between the two. You could mute the headphones by turning off the headphone amp, but the only way to mute the speakers would be to turn off the power amp - feasible, but not something that seems convenient.