The only proper way to hook up subwoofers is with a dedicated two way subwoofer crossover preferably digital. The preamp outputs go to the crossover which will have dedicated main amp and sub amp outputs all line level. This rolls off the main speakers improving integration and lowering distortion in the main speakers.I've had the best results using an external crossover as well. Back in my home theater days I purchased an Outlaw ICBM-1 for bass management in the analog domain, including integration of 2 subs. I kept only the ICBM-1 when I went back to 2-channel. It's been in/out of my systems for years and I still find it to be quite transparent and incredibly handy. OP .. these can still be found used on ebay in the $200-$250 range. Here's a review from back in the day if you'd like to know more about it.
http://www.soundstagenetwork.com/revequip/outlawaudio_icbm.htm