It makes no difference if you switch your connections at the amp end, OR the speaker end. The result will be the same.
I had a similar issue with a passive pre that inverted. I was running a pair of Transparent Super Bi-cable XL, a networked cable. I flipped them at the amp end so I could A/B the results quickly (2 versus 4 spades to switch). Networked or not, it really doesn't matter which end of the cable you flip.