Does your subwoofer have a "high pass" connection? High pass is connected to the speaker terminals along with your speaker cable. This is the preferred way to run a subwoofer for audio in the opinion of many including me. With high pass the sub compliments the main speakers instead of replacing the bass with a crossover.
My speaker cables have spades, so I used bananas for the subwoofer and plugged it in back. If you have not bought a subwoofer yet, take a look at REL. Very easy to connect and integrate with your main speakers.