Would you still want to use something like that if you were running the speakers with a subwoofer? Seems like it would defeat the purpose of the sub to strip the low frequencies out before the amp sees them.
The sub-woofer doesn't strip out anything to the main speakers. Subs just cover the lower range only.
How would it work best with this setup? My NAD C372 has two sets of preamp outputs and one set of power amp inputs. My DAC is connected to the "DISC" input channel. One of the pairs of preamp outputs is connected to the power amp inputs and the other pair of preamp outputs is connected to the sub.
Send one set of outputs from your pre-amp to your sub and one set of outputs to a separate amp to power your main speakers. You can insert the inline filter on the inputs to the main amp. And then don't use the amp built into the unit. Basically you'd be using your integrated as a pre-amp. That is the only way to utilize a high pass inline filter like that.
Would you accomplish the same thing for the desktop speakers by connecting the RCA filter between the preamp out and the power amp in thereby still having the low frequency signal available for the sub via the other preamp output?
You mean looping your pre-amp out into the main amp input? Ah, that is a unique case, but might just work. If so then you could insert the filter there.
Alternately, if I used a sub with a PEQ amp could I connect the DAC to the line level inputs on the sub then connect the sub's high pass filter outputs to the amp for the desktop speaker?
No. For one, you wouldn't have a volume control. Secondly, never use a speaker level high pass out on those cheap plate amps. All they do is insert about a 100uF electrolytic cap into the signal path. That is the worst possible way to add a high pass filter. That will totally ruin the signal to the main speakers.
In this case, since the PEQ's high pass filter doesn't send anything below 80Hz to the amp would the inline RCA filter still be necessary?
Nope, nope, don't use those at all. You'll be reducing the sound of you main speakers to the quality level of a clock radio when you do that.