Does your sub have speaker level inputs? I also use the analog connection for the CD player and use Bypass. Polk Audio suggests connecting the sub via the speaker level inputs. Here is a link to their article. http://www.polkaudio.com/education/article.php?id=19 . On the 990 I set the mains to large and the sub to None so all the LFE and small speaker bass gets sent to the front mains. Then I connect the sub to the speaker level inputs and use the crossover and level adjustments on the sub to blend it with the rest of the system. Some may say that this gives double bass. Not if the sub is adjusted correctly. My main speakers are full range and reproduce freq down to just under 40Hz. I set the xover on the sub to 40 so that it picks up where the mains start to roll off. I tried other configs using the sub output on the 990 and have found this setup to work best for both music and movies. If I only used my system for one or the other I would do things different.