I don't want to make this issue any more confusing than it already is but there is an important difference when using the multi channel analog inputs vs. the 2 channel stereo inputs. The difference is analog bass management which can't be defeated entirely applies only to the multi-channel inputs. This means if you use the 5.1 inputs all bass info below 80Hz in either the left or right channels will be summed and sent to the subwoofer output jack...even with analog bass management rear panel switch set to "off". The dreaded double bass issue raises it's ugly head once again. The solution is to set the switch to on and engage the hi-pass filtering to the left and right signals or leave it off and turn off the sub amp.
Routing the left and right signals from DVD or CD player to a 2-channel input is a better idea in my opinion. With stereo bypass engaged no signal is present on the sub output if the front speakers are set-up as large. Setting them to small engages the digital bass management and will send a summed bass signal to the output based on the crossover settings. This is double bass again since the front signals will not be rolled off but you can control the crossover frequency. Analog bass management is fixed at 80Hz.
Hope this helps.

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Tekdredger