I looked over the Yamaha manual and there is nothing to be gained from joining the sub 1 and sub 2 connections. Both are mono outputs and connecting them together will not increase the output. The second sub 2 out allows you to run separate cables to each sub instead of having to daisy chain from one sub to the next. I'm not that familiar with Yamaha's YPAO but if the AVR manages the two sub outs separately (as opposed to treating it as a single sub channel), then you definitely can not bridge them.
Either run just one mono RCA cable as you are now, or try the speaker outs as mentioned above, but there may be issues with that. To run the subwoofer off of the mains channel you need to disable the subwoofer output on the AVR and run the mains full range. Otherwise you will not get any LFE (low frequency effects) to the subwoofer as LFE information only gets sent to the sub out when a subwoofer is enabled on the AVR. That also means you loose the crossover feature (typically at 80Hz) for bass management and will get some of the same bass frequencies from the sub and mains. I don't recommend this unless it is unavoidable. If the subwoofer is not staying on or not returning from sleep mode then it may be time to consider a replacement. When my Klipsch sub started acting up I knew it was the electronics and had to replace it.
I did think of one more possibility. Is there a level control on the subwoofer and is it set relatively high? If the input sensitivity on the sub is high, then the Yamaha may be sending a lower level signal. You could try turning the subwoofer's level control down and run YPAO again to recalibrate the sub level. Most manuals say to set the sub level around the middle. Try setting it lower than that, rerun YPAO and see if the AVR sends a higher level signal to the sub. That may keep it from going into sleep mode.
Thanks for the detailed response. It has triggered some additional thinking over the issue.
Para 1: Noted. So the wye-connection option is no-no. Even other members are not in favor. So the subject of the thread has been addressed. Thank you one and all. Now for the sub going into standby mode issue.
Para 2 & 3: For the speaker out option I am not so sure of your concerns. You see, the sub has a variable cross over frequency setting. Depending upon the setting, only frequencies below the setting is output from the sub, the frequencies above the setting is passed on to the L&R front speakers. There is no mixing as you apprehend.
The AVR also has a cross over frequency setting. The two cross over settings (AVR and sub) should be coordinated, otherwise there can be issues.
The procedure for YPAO, as per the manual, is that the the sub volume should be set to half and the sub cross over frequency should be set to max, which was followed while making the measurements. The cross over frequency of the AVR will be set by the AVR itself after making the measurements. The subs maximum possible setting is 200 Hz and the YPAO set the crossover for the AVR at 160 Hz (the AVR settable values are discrete and not continuous, you are probably aware, mentioned it just to avoid any discrepancy).
The AVR setting also has an extra bass feature. If set to on, both the sub and the front speakers produce the front channel low frequency components. If set to off, the manual says, "Depending upon the size of the front speakers, either the sub or the front speaker produces the front channel low frequency components. I don't think that this has any effect, because when playing a 5.1 music DVD, if the sub volume is set to minimum, the base guitar sounds flat, in both the options. Of course, this maybe because the bass of the guitar is directed to the sub only by the recording engineer.
My apologies for not having thought of the following earlier, but then the sub going to standby was not the subject of the thread. The problem arises when the AVR's own decoders are being used, for example, when a laptop is connected to the AVR via HDMI cable and the Amazon Prime Video app on the laptop is used for watching a movie, with the AVR decoding set to 'Dolby PL II Movie'. If the DVD player connected to the AVR via HDMI is used to watch a 5.1 DVD, and the DVD player setting for HDMI is Bitstream audio ( as against PCM), then there is no problem.
The sub has an 8" woofer. Each of the towers have two 8" woofers. The manual advises that speakers having drivers of 6.5" or more should be set as large. Despite this, if the front speaker settings is set to "small", then all bass will be directed to the sub, and hopefully it will not go to standby, since the problem happens only when the decoders in the AVR is being used. A short test run of about 20 minutes confirms this, will have to check whether it will work for a full length feature film. Also, tweaking the decoder settings may also work,not sure how to go about it.
Any comments please?