Yep this can definitely be done. All you would need to do is override the main logo with a different one from inside your CSS.
Do you have a link to your site as well as a link to the logo that you want to use for scrolling? You can upload your second logo through the Media uploader, or through FTP.
The header doesn’t change color it should stay Black even when you scroll down. The only time it’s not Black is when being viewed on the Homepage since the header background is Transparent (see through).
BTW, this can all be changed. If you want to keep the header background color and size to stay the exact same at all times just let me know. If you want to keep it as it is, but add a second logo we can do that as well.