All you have to do is set the path in the stylevars..
Collapse the vars list by checking the Hide Variables box and then click on ImagePaths. second from the bottom you will find

You can set the path to your new logo there.
One of the best practices is to never alter the default files like the images folder. Copy it, rename it, and then set the path in the stylevars for the theme you are creating.
The same goes for the default style for vb. Add anything to additional.css, I use
as it ads nothing to the style but will let you download it, If not it says that no changes have been made and it will not let you download the xml.
Install the style as a standalone with no parent and then change the image paths to the copied, renamed, images folder. You can then start building you site theme without compromising the default images or style.