Hooking stereo direct in will only pass stereo to the receiver and no sub information should be present to go to bass managment. For bass information you would have to pass signal through the sub direct in on the back of the receiver. A DVD Audio player will do this and will engage the bass management, a stereo CD player will not. If you want the CD direct AND subwoofer my suggestion is to use the direct L/R front stereo inputs to the CD player and then the L/R Front pre-amp outs to get a signal to the sub and then use the sub's cross over to select the sub's response frequency from the full frequency signal thus derived, as the receiver's bass management would not be engaged in this set up. If you want bass management then the L/R pre-amp signal must be sent to a seperate bass management section (i.e., another receiver) and then sent to the sub through this other device's sub out.
The words are more confusing than the actions.