AD, to answer you in reverse order:

Inputs like the one your sub has are known as 'summing', meaning the signals add together. 99% of the time, there is a resistor in series with each input that are tied together toward the amplifier. Using a Y-cord effectively parallels the two resistor, which halves the resistance. A small adjustment of the input level control would have the same effect, so, no, you don't have to use both jacks.

Whether a brand name cable makes an audible difference has been a subject of debate for decades. If the answer were clear, there would be no debate, so the best thing to do is try for yourself. My personal opinion is that a good-quality cable is adequate. I wouldn't pay $75 for a 24ft. cable, unless I were a millionaire, and even then, maybe. If I were doing a home theater install FOR a millionaire, on the other hand, I might suggest it.

Larry