You will need a line out converter So that you turn the speaker wire's into amplifier RCA's, Then from there everything is as normal. Or you can buy amplifier's with high input's, Connect speaker wires into the high input of the amplifier. But if you ment run a subwoofer direct off the deck............No.
Of course you can, just hook it up in place of any of the other speakers. The fact that it will sound like crap by playing the entire frequency range is irrelevant, but a simple cheap LPF will fix that.