Does one input on the A5+ sound better than the other?
Nope. The 3.5mm stereo mini and RCA inputs run on the same analog circuitry and will sound equally awesome.
Support Type: A5+ Classic Speakers
If I have a subwoofer of my own, how would I use it with the A5+ Classic?
All you would need to do is connect the variable output of the A5+ Classic into the input of your sub using RCA cables.