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.
