A subwoofer is a mono device, and only needs a single channel of audio fed to it. If your subwoofer has a twin stereo input for low level input, this is designed to make the subwoofer compatible with the pre-outs on stereo amplifiers, where the bass for the left and right channels is sent to the subwoofer seperately, and then combined inside the unit.
AV Amplifiers send all low level bass below a frequency cut off specified on the Amplfieir, out through a single RCA phono socket (the 'sub out' connection on the rear of the Amplifier). Therefore, you only need the single lead, from the rear of your amplifier, into either one of the inputs on the subwoofer.
The subwoofer will automatically detect whether it is recieving a stereo or mono signal, and adjust its output level accordingly, so that the volume from the sub remains the same.