If you use all 4 wire cables, and wire the speaker to use the +1 and +2 connectors on the jack plate, then you don't have to worry about which cable you use.
Another option that I would recommend is that since you are probably bi-amping (unless this is just for a bass rig, if it is, ignore the rest of this) make panels for the back of your rack with NL4 speakon sockets. Hook up pins 1+ and 1- to the main amp, and 2+ and 2- to the sub amp, using the terminals with binding posts, or another speakon connector hooked to pins 1+ and 2+. This will give you mains on pins1, and subs on pins 2.
Now wire up your subs with the 2 speakons paralleled, and the wires going to the woofers in the cabinet will be connected to pins2 on the speakons. Pins1 will just pass through to the other connector. Use a short cable to connect the mains to the subs.
You MUST use 4 conductor speaker cable with this setup (at least to the subs), but you'll only have one wire going to the sub, and then a short jumper going from the sub to the main. this short jumper could be 2 wire cable.
I can draw it out later if anybody needs visuals for clarification.
This also allows you to hook up the mains without the subs and just leave the sub amp off if you don't need it for a particular application, since the mains are on pins 1 and they won't use the pins2 of the connector.
Consistency across your setup will minimize errors that could cause down time.
