I am not familiar with Photomatix, but I assume it is NOT a Raw editor.
I am not knocking Faststone, it is a fairly decent editor. Faint Praise perhaps, but it is free. No dispute that it can do the cloning jobs.
But I do think that shooting Raw, but not using a Raw editor, is certainly not getting the best from your pictures.
Raw is a big philosophy, not easy to summarize. I would invite you to watch the video at
Why shoot Raw?
But cameras have many settings available, like white balance, like contrast, like Vivid color saturation, etc. The camera does this processing, and outputs JPG files containing those settings.
Raw is extremely different... Raw outputs a Raw file, meaning, with NO processing of those settings. We do that processing later in the computer, after we can see the image, and know what it needs, and maybe try different things then. Raw editors do that.
Further, there is a bigger difference. In JPG, the camera processes the settings, which mostly involve shifting the data in the RGB channels back and forth (tonal changes). When we edit JPG in a photo editor again later, we may shift it back and forth more. We might change our mind next week, and go shift it back. All this is somewhat detrimental. Every change shifts real data, and replaces the original data with the changed data.
Raw NEVER changes the original raw data. Raw editing simply saves a list of all the changes, and when we output a JPG so other programs can see it, THEN it shifts the ORIGINAL data, ONE TIME, into that output. If we decide next week we want something else, we discard the expendable JPG copy, and go change our list of changes, and then output that result ONE TIME. We are not aware of the list, but that is how it works... called lossless editing. We always start from our original Raw data.
Raw involves several big deals, but it requires Raw software.
Faststone is not a raw editor, so it merely gets the embedded JPG that is in the raw file (which is used to show on the camera rear LCD, and to show the histogram). My Opinion is this is a BASIC JPG, and NOT a FINE JPG, regardless if camera might be set to output FINE JPG files. Faststone totally ignores every aspect of the Raw file, and gets the Basic JPG, and proceeds with that. Might as well be shooting JPG.
If you want to use Faststone, or use any of the camera settings, you should output JPG files.
If you want to use Raw, you should get a Raw editor. Invest in Lightroom, or at least Elements. You will like it.