Your speaker/subwoofer cables don't care about line voltage.
Only your connected equipment needs to be powered at the respective correct voltage.
So, yes, you will be connecting both the speaker cable and the subwoofer cable to your amplifier outputs.-Either stacking the spades or using a combination of spades and banana plugs (I don't know if your amp binding posts allow for that).
Just follow the directions that Johnny gave you regarding set up of the subs and use the WX-2 to dial in the proper settings. Once done, either get the Vandersteen M5-HP or call Johnny and get the fixed crossovers.
The WX-2 is for determining the correct settings and is not supposed to be used as a permanent crossover. When in doubt, either call/email Johnny or Vandersteen. Of course, we'll always try to help...
Bob