Go to Edit Start Menu and Taskbar, Select Horizontal Taskbar (Unless ofcourse you want to edit the vertical taskbar), Select Background under the Horizontal heading, under the Image Tab click Edit image and the image should automatically open in the default graphic that is set to open that particular file type (.jpg, .png, .tga, .bmp). In my case, they're all set to open in Photoshop CS2 -- (makes life easier). Then, once its opened in your graphic program, simply edit to whatever color you like, save it, go back to Skinstudio, import it as the horizontal taskbar background, apply, and your done!
