1a. While I haven’t tried it, there’s no reason I can think of why you could not use channels 7 and 8 as either tweeter or woofer channels for the main speakers, if you run a 5.1 system.

1b. While it is possible to leave the existing crossover in place when you do this, you must remember that anything you do in the active crossover “adds” to what the passive crossover does. So at a minimum you are introducing an additional 3dB of attenuation to both the woofer and the tweeter at the crossover point. You could counter this by moving the filter frequencies away from the nominal crossover frequency (down for highpass, up for lowpass), but it fairly soon becomes a question of why bother… 😉 If it were me, I would remove or bypass the passive crossover, leaving only a protection capacitor on the tweeter.

2. [Edit 27 July 2014] I’ve not observed it as an issue in practice, with an 80-100 Hz crossover frequency. However, the new version of the plugin has a dedicated bass management screen that removes the issue completely.

Hope this helps 🙂

A couple of questions if you don’t mind:
(1) I presume there’s no reason one couldn’t use the unused 7th & 8th channels to bi-amp ones main speakers, using the Nano’s crossover functionality to ultimately (after D/A conversion) send high & low-passed line-level signals for the mains speakers’ treble and bass drivers, respectively, to the amplifier? (in the simple scenario I’m thinking of I’d leave the speakers crossovers in place, but just have the benefits of a narrower/easier frequency band for each amplifier)
(2) I seem to recall reading that the way the NanoAVR’s low-pass filter applies to the sub will mean any LFE info above that frequency (e.g. 80-120hz) won’t be passed to the sub so wouldn’t be reproduced by any channel in the system. Did you observe this in practice?