Depends on the type of sub you are using. If its with a ss system (like a 5.1 logitech) then there is no sub input. They use crossovers inside the electronics. BUt, if you want to go from just the pc to a single sub (this would be if you have a separate amp for the main speakers) then I would take a Y cable to connect it to the low-level input on the sub. (has a 3.5 mm stereo plug on one side for the sound card, and two RCA plugs on the other side, one red, one black or white) By doing this, the soundcard is acting like the crossover, and only sending the lower freq. out to the sub.
Another way to do it (assuming your sub amp has speaker level inputs) is to run the speaker cable thats going from your main amp to your speakers through the sub first. You only have to do this with the stereo speakers (not the ss speakers, as there is only 2 inputs). By doing it this way, the sub is picking up the lower freq. from the speaker wire and sending it to the sub speaker, while letting the higher/mid range frequencies go to the main speakers.