I have the PEQ3 amp, and use line in for music (second output on preamp), and LFE in for HT (separate HT preamp) with great results!
I cannot say it's the best... Honestly, I'm not sure why people are saying line in is better. BUT I have no experience with it, and would love to hear the reasoning!
FYI, it looks like Danny uses Line In, maybe he can chime in with his thoughts on this:
Looks like he uses output 1 on his preamp for the subs, and an unlabeled output for his speaker amps.
With fear of looking like an idiot and exposing my ignorance and likely faulty reasoning, here I go... Wouldn't you want the most unadulterated signal possible for the sub? Why would you want to push it through another series of amplification (and cables) before the sub? Wouldn't this (no amp is perfect...) degrade/color the signal with the amplifiers characteristics to some measure? - I assume the Rythmik amp isn't actually using the full power signal (like your speaker) from the amplifier, and is somehow just reading the signal and amplifying it with the Rythmik amp?... Clearly I don't exactly understand high level in
Also as JackD said:
+
But I haven't found anything from Rythmik saying High Level In is the best for sound quality. Maybe a private conversation with Brian (I think that's his name?) from Rythmik?