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I had run a powered sub with speaker-level inputs in both my 2005 WRX STI and 2007 Subaru Legacy GT, which had a completely non-replaceable factory stereo. Basically, you just run some speaker wire to the sub for audio input, then a separate power/ground. The one i had was an Infinity basslink, but there are a bunch of options now, depending on where you want to put it. Most come w/ adjustable volume and a crossover. Crutchfield has a bunch: