The only subwoofer output goes into the stock 8" subwoofer.
Are you wanting to run both the stock one and your aftermarket one?
If so, I've been told it's not a good idea as it'll cause distortion, underpower etc.
Disconnect the old sub and just solely run your aftermarket one, and you can utilise the stock subwoofer wires (which are hi level speaker inputs)
Check out this thread for my explanation to Matt on how to hook up an additional sub and amp.