Interaction between Sub XO and Amp?

The high pass (to your main amp) is typically applied before the sub's amp. However, the high pass is still another device between the preamp and main amp, so you're dependent on it's quality (although it's just a capacitor, but how good?.) Further, you will have four cable connections between you preamp and main amp instead of two, plus some internal wiring (in the sub) of unknown origin.

If your preamp has two pairs of "main outs", and depending on your main speakers (you didn't say) the ideal way IMO is to run them full range from one set of preamp outs, and run the sub (again, you didn't say what kind) from the other set of preamp outs, just enough to fill in the very bottom that your main speakers miss.

Nsgarch: thanks for your thoughts. The way you describe is how I had my system set up. A friend told me that cutting the lowest frequencies from my mains would provide better clarity in the mids. I tried it (reluctantly) and was very surprised at how much more "slam" my system had, and how much better it sounded in general. It also helped my mains "get right" on piano and some male vocals, and removed a "haze" or slight midrange glare that exists when I have the mains reproduce the full range of sound.

I'm looking at upgrading my sub (currently a Velodyne CT-120, originally purchased more movies) and my speakers are nOrh mini 9.0's (website claims it reaches 45Hz at -3dB, but that's a stretch in my room based on measurements with my Radio Shack tester.)

If your preaqmp has 2 oputputs, run one to the fulrange amp and the other to the sub. That way, there is no risk to the full range signal. This of course, assumes your satellites can handle full range sound well. This will work best if your preamp outs are buffered from each other. This means the 2 outputs are electrically isolated form each other. I have a similar situation, running Entec subwoofers and a Behringer EQ from 1 output, and full range speakers from the others. My outputs are not buffered from each other, so if I make changes to the EQ, it affects the sound of the main speakers. I think only the volume of the sound changes, not the fundamental character of the sound, but it is worrisome to me nonetheless. But the system sounds good, so I won't get too worked up over it. The only way I know of to tell if the outputs are buffered from each other is to call the manufacturer and ask.

What subs are you using? Maybe someone else here has them and can answer more specifically.
Re: your question, the signal will certaqinly pass thru the subs crossover, which could cause degradation. The more complicatred the high-pass portion of th crossover, the more likely there will be degradation. There may be some line-level preamp type gain stages involved, particularly if the sub allows you to do any processing of the high pass signal, such as boosting it's level, changing phase, whatever. I think most subs, though, have this type of control working on the bass, not the rest of the signal.