How to optimize sub integration with 2 channel?

Most subs just have a low pass filter, and allow the main speakers to play at full range. This makes integration relatively easy. Other subs, however, also have a high pass filter for the main speakers, allowing you to relieve the main speakers from the stress of having to reproduce the lowest frequencies. The price for that, however, is more complex integration.
If the sub of your choice does not have an inbuilt high pass filter (these days few do), you will have to use an external cross over/high pass filter. Interestingly, many pro audio amplifiers have precisely such a high pass filter. And some of those pro audio amplifiers are very good, at least as good as some audiophile amps, though for much less money (thanks to economies of scale and lower mark ups). So that may be one way of doing this. Another far more expensive way would be to get the forthcoming DSPeaker X4 DAC/Preamp/crossover/room eq.
In any case, with subs I would always recommend having at least two (in mono) for a smoother in-room response, augmented by dsp room eq like the Antimode 8033.

Just discovered that the Swarm system also includes the possibility of high passing the main speakers.

Subwoofers can be as small as they are by using big amplifiers and using them to boost the signal, the lower the frequency. However, there are limits to this if you do not want to have too much distortion, or destroy the driver. Therefore, increasingly subs have complex dsp to do this without overpowering the driver. So maximum spl is monitored, and so is frequency response. Not sure what the Zu does exactly, but my B&W PV1d reduces the low end extension more and more, the louder you play it, to keep the driver within comfortable limits. So there is little point in bypassing this. It does not look like the Zu dsp has anything to do with dsp room equalization of the kind built into e.g the bigger Velodyne subs.
High passing a sub only makes sense in two very specific situations. The first is if you cannot play the system loud enough, either because your amplifier does not have the power, or because the speaker cannot handle more power. If that is the case, highpassing the main speakers and main amp makes their life a bit easier. The second issue is related, if the speaker distorts too much when played loud. Speaker designers can increase low fequency extension, but at the expense of increased distortion. If you do not like the balance that was struck by the speaker’s designer, reducing the burden on the main speakers helps. In short, in normal situations I do not think there is much point in high passing the main speakers, given the disadvantages. And I would certainly not want to spend big money on addressing the shortcomings of an amplifier or speakers.
The Zu looks like a pretty ordinary though perhaps a bit expensive subwoofer. But I have never heard it, nor would I think that a listening test would have helped me much. Subwoofer sound is largely determined by the room they are in, and by the room modes in that room. Listen to them in a demo room, and you have heard the sound of the demo room rather than of the sub. It is for that same reason that I think multiple smaller subs are far preferable, because they smoothen the response, and even so preferably combined with dsp room equalization by a unit like the Antimode 8033. See here for some introduction: http://www.acousticfrontiers.com/20101029using-multiple-subwoofers-to-improve-bass-the-welti-devanti...
For that reason, you may want to consider the Audiokinesis Swarm System, but always in combination with dsp room eq.

Since you already have a sub, I would suggest getting a DSpeaker Antimode 8033 first, for room equalization. You will be pleasantly surprised by the improvement. See here for a review: http://www.theabsolutesound.com/articles/dspeaker-anti-mode-8033-dsp-subwoofer-equalizer-tas-204/
I am not quite sure about the kind of connections you have, but if you have a line level output from your amplifier, that should work just fine. Get the 8033 Cinema in that case.