I forgot that it was also a headphone jack. I don't think there's a way to stop it from shutting down the speakers when you plug something in. Possibly a way to use your sub-woofer is to attach an external USB sound card. Here's an example of one that should work.
Shop for your Apple, Mac, iPhone and other computer products on Amazon.
We are a participant in the Amazon Services LLC Associates Program, an affiliate program designed to provide a means for us to earn fees by linking to Amazon and affiliated sites.