Ok, I think I just talked only about the nopCommerce logo. If you want to change the backgrounds (note:plural), you'll have to go into various CSS files in your theme folder. Base.css has the body class that will change the background on the very bottom layer.
Keep in my mind all the content are loaded on as layers in div wrappers. Each wrapper could have its own background. You'll have to change each background to transparent or what every you want. I put a tiled background on my body and then a centered watermark on master-wrapper-page and change most of the background to transparent.
Don't forget that things like searchboxes or text entries have background that should contrast so you know where it is.