software settings. if you're using a laptop or an OEM PC (HP, Dell, etc) then it will most likely have a single 3.5mm stereo output jack. if you're using a dedicated soundcard then chances are it will have at least 4.1 surround (4 separate channels plus a subwoofer output). using all 4 channels can be a pain to configure. even if you have 4+ channels available, it is often times preferred to set your sound card's settings to "2 speaker stereo" and simply use a y-adapter to split the 2 channels into 2x2 outputs (2 lefts and 2 rights, front and back play the same sound)
parallel you cut their impedance in half, when you wire speakers in series you double their impedance. when you lower the impedance you raise the amp's output power, when you raise the impedance you lower the amp's output power.
most amps are 2-ohm stereo stable, so if your speakers are 4-ohms each you can wire them in parallel and the amp will see a 2-ohm load. since you are using your stock speakers, you need to find out their impedance before you can determine how to wire them up. if your amp is 2-ohm stable but your speakers are 2-ohms each then wiring the speakers in parallel will give the amp a 1-ohm load (which may burn the amp out), wiring the speakers in series will give the amp a 4-ohm load (which is fine).