I assume you play your CDs in the DVD player.
Your DVDs playing with 5.1 audio use 6 tracks for sound including the track for LFE and low frequency sounds which are directed to the subs subject to your Crossover setting (80 Hz, 100 Hz?).
As for your CD playbacks, even though CDs are in stereo, whether the connection between the DVD player and the Yamaha receiver, is digital cable (optical or coaxial) or 5.1 multichannel analogs, the low frequencies should still go to the sub except that low frequencies, when using multichannel analogs, are 10 dB lower in sound volume compared to other tracks. To compensate, you can increase the GAIN at the sub by 2.5 o'clock setting on the GAIN dial. So if the normal GAIN setting is "12 noon", increase this to "2.5". Or you can toggle from multichannel analogs to digital and play them either in stereo or use the following DSPs: either Pro Logic II: Music or (DTS) Neo6: Music and in both cases all speakers will be used although stereo effects are unaltered.