The pre does invert so you compensated by reversing the speaker leads which is good. That should put them in polarity if the sub does not invert polarity. If you are still concerned get a test CD that has a tone near the crossover frequency. Try your speaker connections both ways and the one that is louder at the listening position is the one you want.
However, you also have the issue of the subs possibly being a different distance from you than the speakers. So even if they are in phase at the drivers they won't be when they reach your ears. Not completely inverted polarity but out of phase by some degree. No easy cure for this other than getting the distance as close as possible or using some type of digital delay.
However, you also have the issue of the subs possibly being a different distance from you than the speakers. So even if they are in phase at the drivers they won't be when they reach your ears. Not completely inverted polarity but out of phase by some degree. No easy cure for this other than getting the distance as close as possible or using some type of digital delay.