The issue in relation to the sub's use with stereo audio would depend upon the speakers own ability to handle low frequencies. There's no real need to utilise a subwoofer within a dedicated stereo setup that utilises full size cabinet speakers because you will in all likelihood not be using the small and diminutive sat speakers that have become more synonymous with home theatre packages. It is only these speakers that need a sub to cover for their deficiencies. A movie will include anLFE channel that carries frequencies below what you'd expect to find in association with stereo audio and this is why the sub is more important in relation to an AV multichannel setup than it is to a dedicated stereo setup. If you had floorstanders then you'd not need the sub in relation to 2 channel stereo content, but its use is still required in relation to multichannel audio that includes an LFE channel. Many dedicated stereo setups run perfectly well without a subwoofer being present. It is suggested that a crossover of 80Hz be used on AV receiver in relation to the sub pre out, redirecting all frequencies at and below this point from the speakers to the sub, but many diminutive sat speakers can't even achieve frequencies below 120Hz let alone 80Hz. It is the use of such speakers that has given rise to the belief that every setup needs a sub even in relation to stereo 2 channel content.
I'd suggest you try to use Q Acoustics speakers throughout with the option of a BK Gemini sub as an alternative to the Q Acoustics 2070 sub. The Yamaha speakers are nothing special and the only real reason to buy them is if you cannot afford something better? Using a different sub in conjunction with them will not improve their abilities in respects to their mid and hi frequency handling abilities. The Q Acoustics speakers will award you better mid and high frequency performance than the Yamaha speakers and this is the reason why I suggest the Q Acoustic speakers over the Yamaha speakers.
Regardless of whether you've a stereo or a multichannel setup, the speakers will be heard and used far more than the sub. Their quality should be addressed before addressing the subs abilities because the speakers will play a larger part in how the setup sounds than the sub will. The QA speakers are better than those included with the Yamaha package.
Another viable alternative to the QA 2070 or Gemini sub would be this:
Wharfedale Diamond SW150 Subwoofer (Black) - Superfi