In short, you use a photo/raster picture editor like Photoshop. Gimp and Paint.NET are free editors. Photoshop and Gimp require plugins to open DDS files, whereas Paint.NET includes DDS support out of the box. There are additional tutorials in the tutorial section that discuss how to replicate Firaxis' style for civilization icons, unit and building icons, leader diplo screens, intro civ maps (look for "Sukritact's Cartography Outline"), and how to reskin units.
If you are trying to edit the indexed DDS files (where filename-index.dds accompanies filename.dds; this is mainly for user interface stuff, so you probably won't need to worry about it), then you need to use this tool to first convert them to PNG so you can edit them and resave them as regular DDS files.
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