Terrain artists seem very scarce in the community, I can't even name 5 people capable of doing it including me. It's really not as hard as one might think it is, all it requires is some basic knowledge of how your photo editing program works (Photoshop, PSP) and a lot of patience.
In this tutorial we will change the basic temperate clear tile into something different. What you need are the original .tem files, a texture image of your choice, and a photo editing program. In this case, we will be using Photoshop. I'm sure there are counterparts for every used feature in Paintshop Pro.
First of all, locate the clear tiles in XCC Mixer and extract them (clear01-clear01g.tem in isotem.mix).
Then open Photoshop and load the desired texture. Textures can easily be obtained from google searching or from Generals. Let's assume you want it to be the same color as the clear tile, so it blends in with everything else. Photoshop's Match Color tool is extremly useful for this (Only available in Photoshop CS and above). Open FinalSun and make a new blank map filled with the tile you want to edit, take a screenshot, paste as a new image in Photoshop and crop out an area with just the tile. Now select your texture, go to Image > Adjustments > Match Color then pick the FinalSun screenshot as the source. You should preferably lower Color Intensity down all the way.
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Excellent, it is now using the same color as the tile. Now we should give the texture an isometric perspective. To do this, first go to Image > Rotate Canvas > Arbitrary and rotate it 45 degrees either clockwise or counter-clockwise (Doesn't really matter). Then resize the image heigth down 50%. After changing it around it may lose some detail and look blurred. To fix this use the Sharpen effect. Usually it gets a bit too sharp, so use Fade Sharpen in Edit and bring it down to 20-40% or so until it looks good enough.
We're all done there now. Next we open TMP Editor which is included with XCC Utilities. Load clear01.tem, copy it, and paste as a new image in Photoshop. Now you simply select a random area from the texture and copy it over as a new layer onto the tile. It will cover some unwanted areas, this is easily fixed by simply going back to the tile layer, selecting the transparent area with the magic wand (Make sure tolerance is set to 0 and that anti-aliasing and contiguous are off), go back to the texture layer and hit delete. You may want to play around with the blending capacity after that, but that's entirely your choice. Now press CTRL+E to merge the two layers into one, and it's done!
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Now just press CTRL+A to select the entire image, copy it, and paste it over the original tile in TMP Editor and save it. Now just repeat the same process (And preferably select different areas on the texture each time) on each tile until they are all changed. You'll get the hang of it soon enough and it'll be a second nature.