Logo designs are usually created with vector image editing software, not raster image editors like GIMP/Photoshop/Paint.NET. Using a vector image editor would be much better, especially if you want to customize colors in a logo, since it would just be a matter of changing the color of the fill in the parts you wish to change.

The top selling vector image editor is Adobe Illustrator, but it's expensive. Inkscape is Open Source, as GIMP is, so it's free http://www.inkscape.org

Here's a screen shot of Inkscape showing how you could easily customise a logo with new colour fills