SPEAKER menu items are on pg50 of Yamaha RX-V381 Manual. Be sure that Sub-Woofer is set to "USE" and all speakers set to "SMALL" in order to direct Low-Freqs to the Sub-Woofer. My Rule of Thumb to minimize Distortion is to set the CROSSOVER Frequency to TWICE the -3 dB Roll-Off Freq for your L/R Speakers, which is "typically" 40-Hz, hence 80-Hz is the DEFAULT [unfortunately, many mfrs fudge their Low Freq Roll-Off Specs so the actual -3 dB Freq might be a bit HIGHER than Spec]. If your L/R Speakers are smaller than "usual", check the specs to see if you need to select a higher CROSSOVER Frequency. [Sadly, your AVR does NOT allow for selecting different CROSSOVER Freqs for different Speakers....so you MIGHT need to use a higher CROSSOVER Frequency to reduce Mid-Band Bass Frequency Distortion coming from the Surround Speakers:
Note that there is an optional "EXTRA BASS" selection (Default = "OFF"). You should NOT need to turn this "ON"
, since it directs Low-Freqs to L/R Speakers in addition to the Sub-Woofer, which Increases rather than Decreases Low-Freq Distortion. [As I understand from reading other Manuals, your Manual is Silent wrt WHAT it really does]. After making sure that everything is set-up as it should be, you can turn this feature ON/OFF via the "BASS" button on the Remote Control. You MAY need to do this to hear BASS when playing a 2-Channel Source (whether STEREO Input....or DD2.0 Input).
You should normally be using STRAIGHT mode (w/o DSP Enhancements), although when playing back a STEREO Source Program
you might want to ALSO try some of the Synthetic Surround Sound modes....it MIGHT also improve the sound coming out of the Sub-Woofer....
You should enable TEST TONE (Manual pg52) to verify that all Channels, incl. the Sub-Woofer are indeed WORKING and at roughly equal strength. Since it is possible that YPAO has messed up the Sub-Woofer Level Controls you should first DISABLE it [EQUALIZER = OFF, also on pg52]. With EQ disabled, it's a good time to adjust the Sub-Woofer's Level Control to make sure that it is in the right Ballpark, BEFORE you Enable Room EQ and perform YPAO Room Equalization one more time....