With a setup like this, you definitely want to disable the crossover in the subwoofer, so set the Crossover switch to None. The RX-V2400 (reviewed here) is performing the crossover duties, which direct the frequencies below the crossover point to the sub. (In the RX-V2400, you can set the crossover to 40, 60, 80, 90, 100, 110, 120, 160, or 200Hz; 80Hz is the default and most common setting.) If the sub's crossover is engaged, the signal it gets passes through two crossover filtersone in the AVR and one in the subwhich can make it sound weird. If you disable the sub's crossover, that should fix the problem.
For those with a subwoofer that has no crossover on/off switch, set the sub's crossover frequency as high as possible and make sure the crossover frequency in the AVR is lower than that. This is not ideal, but it's the best you can do.
The Polarity switch controls the phase of the subwoofer, which can potentially help even out some irregularities in the bass of the system. Try it in both positions and see if there's any difference in the bass performance. If so, use the setting that sounds better.
If you have an A/V question, please send it to firstname.lastname@example.org.