What does it say in the receiver manual?
You should only use one of the sub pre-outs on your amplifier to connect your subwoofer. You shouldn't need two because the subwoofer is monophonic. The reason why your amplfier has two subwoofer pre-outs is in case you wish to use two subwoofers in your home-cinema set up. Also one of the pre-outs might be inverted relative to the other, which I think means the same thing as out of phase.