Amp recommendation and setup advice please

The gain setting on the DAC just dictates how loud the output will be.  I would say to use Low or High unless you feel that the sound does not get loud enough.  You do have a volume adjustment on the back of the Yamaha, so I think any gain setting will work.

Select the Fast / Slow volume control characteristics.
        H: Fast.  64 steps range.  
        L: Slow. 100 steps range.
        F: (Full ) High gain mode. 100 steps range. (For the low sensitivity headphone like the HE-6 or the source had low output voltage level)
        S: (Super)High gain mode. 64 steps range. (For the low sensitivity headphone like the HE-6 or the source had low output voltage level)

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Relating to the clarity of the sound, make sure that the setting switches on the back of the Yamaha are all set to "FLAT" or "0".  The switches are not always in the middle position for FLAT/0.  If this is the case, you can try doing a "+2" setting on the MID EQ or the HIGH TRIM.  This may increase the clarity of the mids / highs for you.  Play around and see what you like the best.  Alternatively, you could try Audioquest interconnects that have the silver-plated connectors (such as Mackenzie or Sydney).  Silver plated will give faster mids/highs, but may be leaner on the bass.  In my opinion, gold plated connectors sound more natural, but it's all personal preference.

Movie/television soundtracks are mastered with a 5.1 system in mind.  Unfortunately, you might have to live with the sound if you want to keep the DAC.  Also, the Audio-GD DAC will not support a center channel.  Way back in the beginning of this thread, I tried recommending doing an HT processor or receiver, but it seems our discussion went towards a 2-channel DAC.  Sorry about that. 

If you really want a center channel, you could just get an HT receiver to do the dolby digital / dts decoding for center speaker and use different cable for Yamaha (maybe a RCA -to -XLR adapter cable).  Then use the Audio-GD DAC for your own high end system. 

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If you feel okay with the general sound quality and just want more low bass, the subwoofer idea is good.  The Klipsch R-112SW appears to be a good choice.  Yes, having two subs is better than one.  This allows you to place them in different locations and works better to handle room nodes.  Generally, a room will have bass NULLS, which are areas / frequencies where the bass waveforms cancel each other out from wall reflections.  Having two subs will help reduce these cancellations and give you better bass.  The Klipsch have RCA inputs, so you just need RCA cables and use the standard RCA outputs of the DAC.  You can use both the RCA and XLR outputs at the same time.  The XLR will go to the Yamahas.  The RCA will go to the Klipsch sub(s).  Then just set the crossover on the subwoofer to something like 40-50hz and adjust the gain on the subwoofer to your preference for bass.

As far as room, sometimes we are at the mercy of furniture and other restrictions.  Generally, I think the best would be to put the left/right speakers on the short wall for best sound, but other things may prevent this.  If you get subs, it is definitely best to try to put them into the corners to boost the bass.  Having speakers set in the middle of the long wall is definitely going to produce weak bass (in my experience).

There are other subwoofers you can get.  Look at these on the ebay UK site:

https://www.ebay.co.uk/b/Speakers-Subwoofers/14990?Configuration=Single%2520Subwoofer&rt=nc&_sop=3&_udhi=500

There is a Revel B120.  Also, several BK subs so that you could get two if you wanted.  Or just get one to start and put it as close to the corner as you can get.  If you get two subs, use Left RCA for one sub and Right RCA for the second sub.  If you only get one sub, use both left/right RCA into the same sub.

You can play with the Yamaha's position.  I think generally, you need a little bit of space away from the wall (at least 1-2 feet) because the bass ports are on the back side of the speakers.  But I think the best bet would be to put a subwoofer in each corner. Then set them at about 80hz (the Yamaha's may not play that low when in the middle of the wall).

I can understand your concern on the "split" of the Audioquest cable.  It is definitely not that wide, and the left/right RCA outputs on the Audio-GD are spaced far apart.  I would look at the Belden 1695A Coax cable for subwoofer.  These come in single cables, so you can get two of these (one for each corner sub).

https://www.bluejeanscable.com/store/subwoofer/index.htm

The 1695A uses a solid-core 18awg copper conductor.  In my opinion, this would be an excellent cable for transferring bass frequencies.  Smaller awg conductors do not transfer bass as well.  In my testing, 20awg seems to be the best overall compromise - small enough for high frequency detail, but still large enough for good bass.  When going to smaller 22awg conductors, I get much leaner bass and too much bright highs.  The Audioquest interconnects typically use 21awg conductors.

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There are definitely counterfeit cables on ebay and stuff.  The Kimber Cable speaker wire is very easy to counterfeit because you cannot tell the difference - it's just braided wire.  There are other Furutech connector counterfeits.  Lots of counterfeit junk on ebay from China - stuff that is "too good to be true".  However, buying something like used Audioquest on ebay or elsewhere is usually pretty good.  I have not seen counterfeit "equipment".