I had read that connecting the single sub output jack may not be the best why to set up the sub because when listening to music in stereo mode a signal may not go to sub out jack, Also the sub woofer output jack is low-pass filtered that blocks sounds above a given frequency from getting out of the sub out jack and would degrade the sound
hondo164, welcome to the forum. I'll see if I can help. Things depend on how you set up the bass management in your Yamaha. Your receiver will have the option to set the front/rear/center speakers as "large" (full-range, so bass is not sent to the sub) or "small" (which directs bass below the cross-over point to the sub). You should be able to set those up independently (e.g. fronts are large, center and rears are small).
If you set your front speakers to "large", then bass for the front speakers will not be sent through the sub unless you set it up to send bass to both the sub and front speakers (if you can do that...my older Yamaha receiver had that option).
So, if you have your front speakers set to "large," you have the center and/or rear speakers set to "small," and you only direct bass below the cut-off frequency to the sub, then the sub would play for multi-channel audio but not for stereo audio...just like you read about. That's because in stereo, only the front speakers are used, and you set up the receiver not to use the sub for those speakers. You really should only have the front speakers set to large if they handle bass, anyway, and if they can handle bass...then you don't need the sub working during stereo playback. However, if you have your front speakers set to "small," then your sub will also play for stereo audio. The low-pass filter is not really an issue if you have the cross-over set well because your front speakers will be able to play all of the frequencies above the cross-over point and your sub will play all of the frequencies below the cross-over point.
Hope that helps. If not, let us know. Someone here will be able to help you.