Let's start this reply off by saying that there are several very good options available to do what you want. In fact, today I would say you would be hard pressed to find any of the major RAW converters that will not do a reasonably good job with the X-Trans sensor's files. So your decision is likely to come down to more a question of your own personal preferences and desired workflow as much as anything else.
As to which is the "best" RAW processor, that is as great a debate as trying to decide who to blame for shutting down the National Park System just as fall is almost here. There are plenty of supporters on all sides, and none of them are wrong. You don't say if your shooting JPG or RAW, so i will error on the side of caution and assume RAW given your stated desire for ultimate high quality.
The "Big Dogs" in the pack are of course Lightroom and Aperture. Both now do a decent job. I use primarily Lightroom, but own licenses to both. Lightroom has better digital asset management features for my commercial work so I have stuck with it. However, there are a couple of the "lesser known" software packages that while not as widely installed as Lightroom or Aperture, do as good or in my opinion, an even better job of the actual RAW conversion.
These would include Capture One, which since Ver 7.0.2 has done a remarkable job with the Fuji X-Trans files. Brian Griffith's Iridient Developer (formerly called RAW Developer) also does a remarkably fine job in it's latest release, and is my own personal favorite when I want to take the time to get the very best possible from an image file. I am also quite impressed with PhotoNinja, which I am currently reviewing. Any of these choices would be a good one for you to make, all far superior in my opinion to the SilkyPix supplied with the camera.
As far as camera settings go, here is the way I see it. Cameras are for capture. If your shooting JPG, then you need to setup options such as sharpening, contrast, color balance, B&W settings possibly and saturation to your preferences so they can be "baked" into your final JPG file. You have no choice, the JPG is the final form.
If your shooting RAW files though, you will want a different setup in camera. I shoot my RAW files very flat and a bit dark. To me, the power and control I have in my laptop computer far exceeds anything I mite have in my little Fuji starting out, never-mind that little silicon chip beating at the heart of my X-E1 is plenty busy just capturing and saving to card. So I want all of my post processing, effects, adjustments, sharpening, etc done on the best box for it - my laptop or desktop.
I've found also that anytime I start adding in-camera post processing steps two things invariably happen. The first one being a final image file that is not as good as it could be if I had kept the file clean and flat, doing the final workup instead on my computer. Shoot a few tests for yourself, and you will see what I mean. A flat file will sharpen up better from RAW than one already sharpened in camera, and without ghosting or banding that in camera sharpeners are famous for.
The second thing I have found is without exception, I have regretted later any in camera control adjustments that could have been done in post. Anything you adjust in camera remember is baked into your display, but not necessarily baked into your file if you are shooting RAW. JPG, yes, RAW, not necessarily. All too confusing frankly so I just keep it plain Jane dull and simple in camera. If I want to get tricky or experimental, I can always do that sitting in front of my computer, not standing in front of my subject.
Your own mileage may vary, and I am quite certain others may hold a different set of opinions and options for you to consider. :thumbup: