How to Wire The Speakers?

Hi, here is the list of equiptment I have:
Pioneer Elite A/V Receiver - VSX-92TXH.
NHT 2.5i Main Speakers (Bi-Amplifiable/Bi-Wireable).
NHT SuperOnes (Used as Surround Speakers).
NHT SW2 Passive Subwoofers 2pc. (With Built in Crossover)
NHT SA-3 Mono Sub Amplifier (250Watts RMS).
NHT AudioCenter
I have connected all the speakers to receiver except the subwoofer and mono amp. Everything sounds perfect. Today I have received my SW2 Subs and SA-3 mono Amp and have to connect them to the system. I am little confused in connections now and need someones advice. What's the best way to connect the subwoofers and amp and run the wires through the main speakers? As far i understand, the main speakers' low Freq has to be wired to the SA-3 Amp, then the Subwoofers' have to be wired to the same Amp too. Then the SA-3 Amp has to be wired to the receivers' Preamplified Out. The Hight freq of the 2.5i Main speakers has to be wired to the Main out terminal or the Receiver. (The center and suuround speakers are connected allready to their terminals in the back of receiver). Is that a correct and the best configuration?
Now, I connected the subs to the amp and the amp to the preamp out of receiver today, but the subs were only making some strange whooooo sound and there was a huge delay of sub response.
As I mentioned the subs have built in crossover. In the rear of subs in the connections plate there are 4 pairs of connections. Here is the pic. http://www.blackswampaudio.com/Images/Inv/353.2.jpg
The jumpers you see in the top terminal i remove them for bypassing the subs' internal crossover.
Please, give me detailed wireing instruction for this config.