Customizing colors is fairly easy. After grabbing some embed code from the Publish Links interface, look at the url that reads "http://affiliateexchange.org/linkgen/.../". The URL components following "/linkgen/" are parameters which tell the generator what to do.
The first two parameters identify the affiliate and the template being used, but forget about those for now. Anything after those two numbers corresponds to color information. If you're using an image(s)-only template, all you get is a background color. If you're using text links, you can control the link color as well. With extended text links, col_text corresponds to the color of the website description.
To manipulate color display, simply replace the placeholders (like col_background) with actual colors. You can use either color codes or standard color names in URL requests to the link generator. Please DO NOT prefix color codes with a number sign (#) — it will be added automatically if the link generator detects a hexidecimal color code.
If you don't provide color data when calling the link generator, or you leave in the placeholder values, default values will be assigned. Note that the default background color is transparent, but IE will display it as white. IE will render it properly if you add allowtransparency="true" to the iframe element, but strictly speaking this is nonstandard HTML and will impede validation.