Amp recommendation and setup advice please

The phase switch can help with blending in bass with the main speakers.  You can try both ways and see what has better/more bass.  The phase essentially switches the polarity of the woofer.  If the signal is normally pushing the woofer out, the phase switch will pull it inwards instead.  This can help if the subwoofer is placed further away from your listening position than the main Yamaha speakers.  For example, if you are sitting about 8 feet away from the Yamaha speakers, and the subwoofer is about 11 feet away, some of the bass frequencies from both Yamaha/subwoofer can cancel each other out.  It will just take some listening tests for you to determine which phase switch setting works better.

As far as acoustic treatments, I have used them heavily.  I have about 14 acoustic panels in my own room, including several types.  I have broadband, somewhat narrow band, panel/membrane, and tuned membrane.  It just depends on what you're after.  If you like the way your system sounds, maybe it's best not to start spending.  Acoustic panels can help things, but they can also hurt things.  If you feel you are having bass nulls, it's extremely challenging for a bass trap to treat anything under 90-100 hz.  The GIK Acoustics Monster Bass Trap with FLEXRANGE limiter does an effective job down to about 80 Hz, but does not absorb the mids/highs as much.  If you need something under 80hz, the only real way is to get a tuned membrane traps (such as GIK Scopus).  It's a challenging area. 

In general, some acoustic panels can help, but it's easy to put too much in and all of a sudden the room becomes to dead sounding (not exciting enough).  If you want to play, in your room one idea would be to put broadband panels behind the Yamaha speakers to reduce the echoes bouncing from the back wall to the front wall.  Since you have the speakers on the long wall, I don't think you will have "first reflection" problems.

As far as other tweaks, we can get into fuse and power cord upgrades.  If your interested, let me know and we can start a discussion, but of course it means spending more money. 

fuses - fuses can change the character of the sound in your audio equipment.  The stock fuses are usually bright/harsh/tinny as they have a lot of electrical resonance.  A few fuses I would look at:  Isoclean, Furutech, PADIS.  The Isoclean are made from gold-plated copper material.  They have a nice warm sound and can help take the edge off of harsh sounding electronics.  They can rolloff some of the high frequencies in some equipment.  The Furutech fuses are completely opposite - as they are very fast and very transparent.  Very strong deep tight bass, lots of extreme clarity in the upper mids and highs.  The Furutech are rhodium plated, which can be a double-edged sword in the sense that it can reveal flaws in your equipment (such as bad power cord, poor power supply, poor circuits, etc.).  They are the highest resolution fuses, in my opinion.

The PADIS fuses are just about directly in the middle, but still significantly better than any stock fuse.  They are not so warm and slow as the Isoclean, but not as fast and high resolution/sweet as the Furutech.  They are very cheap at $25USD plus shipping.  You can get them on ebay and they are shipped from Germany.

There are other fuses - Hi Fi Tuning Supreme (which is silver -- I don't like these in audio circuits, but they are excellent in digital transports).  The Synergistic BLUE fuse has been getting very positive reviews, but they are extremely expensive.

I can't see any way to replace the fuse in the Audio-GD.  The Klipsch subwoofer uses a small 5mm x 20mm size fuses - 5A for 110V, 4A for 220V.  The Yamaha uses a small 5mm x 20mm 2.5A fuse, but you can just use a 3A.  The Yamaha fuse is inside on the circuit board, which requires you to disassemble the box.  Removing the tweeter/woofer and then taking out the plate amp is required to replace the fuse.

Please be aware that there are several naysayers and unbelievers on this forum about fuses - they have a tendency to very negatively attack any conversation about fuses -- at that point, the discussion goes into a toilet with a huge argument.  Just warning ya.