Sub Questions: Speaker-level vs Line & Crossover

There are advantages/disadvantages to both.The speaker level inputs will allow the main amps' character to extend to the subs.The "dis" of this is that you may need to position c differently/phasing to accomplish integration.
The Line-level,via the pre-outs will have only one amplifier and less electronics in the loop.You may also find that an IC that is good for the top/mids is not as good at "purly" bass reproduction.
I use the Parts Connection?MAS for the system ICS and Blk Mt Pinnacles for bass,as this is where the come into their own.Just something to consider-YMMV.

I think you are right on! No need for using pre-outs, many believe the sub will integrate better with the speakers when you run speaker level. You might want to explore using Rives test CD and Radioshack SPL meter ($50) when you set the sub up (placement, volume level, and crossover rolloff).
Good Luck!

Your cables will be OK, so don't worry about this. I checked both the Velodyne and a Stereophile review of the NHT 3. I am a fan of minimonitors and subwoofers and my general recommendation would be to experiment with the several options you have, but I would also strongly suggest that you should not stop short of getting all the benefits of the Velodyne digital technology you paid for. Subwoofer technology has come a long way and Velodyne is one of its main pushers.

The first option is your idea of running the NHTs full range and augment their bass with the Velodyne via the speaker level connection. This is OK and probably the easiest way to go.

The second (better) option is to passively cross the speaker and subwoofer at a reasonably high frequency that would allow you to get the full benefits of Velodyne's room correction. For this you could use the Velodyne's built-in 80Hz high-pass filter or maybe purchase a set of ACI passive 85Hz high-pass filters and set the Velodyne's low pass accordingly (the ACI filters should be a bit more transparent than the Velodyne high pass). Apart from the room correction, there are several benefits with this approach, such as allowing the NHT woofer to only reproduce upper-bass and midrange frequencies, thus greatly diminishing harmonic and Doppler distortion.

The only caveat is that you should place the subwoofer somewhere between the speakers and at the same distance from the listening position in order to avoid subwoofer localization cues (until you buy a second Velodyne ;). If you email me (val at dorta dot com) I would gladly send you a couple of articles I wrote about the use of subwoofers with small speakers.

I agree with Vladimir. I run my subs from the speaker terminals, I would get passive filters rather than use the sub crossovers. I have used several electronic[active] crossovers and could always hear them.