You are right, once you have finished editing in Visual Style Builder and downlaod the skin, you could edit by yourself the CSS and sprites using Photoshop.
In your case you need to edit both png and gif files, as the png is used for cases when enable shadow property is set to true and gif is used when shadow is not enabled. You should ensure that solid color and gradients are same in both files. Once you match the desired colors you could save it and use your custom skin, which will be both created with Visual Style Builder and manually. I think that Creating RadWidnow Custom Skin
cloud be also useful.
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