The dev's did say that the style properties system isn't quite complete so that may be part of it.
Due to unforseen circumstances, we have been unable to move portions of the CSS that drives the XenForo style into the Style Properties system as planned. However, this task is near the top of our priority list and we expect the style to be fully propertised in the next beta release, which we will make in the coming days.
You can place it under any directory as you wish to as long as you fill in the location of your logo Image path correctly. You can even create a new directory just for the logo itself. It's all up to your own wish.