I've recently started using the time alignment features of Hijack (v426, built for ext3), and I feel it has noticeably improved the soundstage in my car.
However, something recently occurred to me.
Since the empeg lacks separate, non-fading subwoofer outputs, am I not now 'smearing' my bass?
The low frequency signals come out of the empeg in stereo, but now (via Hijack) slightly offset in time (and therefore phase). When they are later recombined to mono in my subwoofer amp, each discrete bass note now spans a slightly longer period of time. Am I hurting my bass performance by using this feature?
I haven't done enough critical listening yet to know whether any differences are actually audible.

Thoughts? I'd kill for a non-fading subwoofer output on the empeg harness.

Depends on the frequency range used by the subwoofer. Yes, any time alignment change here will have a tiny impact, but it shouldn't be noticeable until the time alignment value is large enough to impinge upon the woofer frequencies.

If your SW, for example, cuts out for anything above 100Hz, then any time alignment value below 10ms is unlikely to be a problem.

Cheers