You can use either, or both, of the subwoofer pre-outs....they're the same. Or get another sub and hook that up, too Likewise you can use either of the L or R inputs, or both. It's up to you. If you have one cable pick one of the sub pre-outs and one of the inputs.
"I realize that somebody playing free music isn't as commercial as a hamburger stand. But is it because you can eat a hamburger and hold it in your hand and you can't do that with music? Is it too free to control?" - Don Van Vliet (aka Captain Beefheart) discussing commercial success in the music biz
Your AVR is capable of driving two subwoofers. When you have only one, you use only one of the outputs. You also only need to use one of the inputs on the subwoofer. You can use a Y-adapter on the subwoofer if you want.
The manufacturer is trying to make the subwoofer as flexible as possible to appeal to as many customers as possible, and it costs them very little to do so. Some people have equipment with no subwoofer output and need to derive the signal from the left and right front channel signals.