According to the Using a Tracing Image for Page Layouts documentation, there is a way to use a tracing image to create a page or page template in Site.com.
Import the image. Open the page template or site page. Select the image in the Tracing Image list in the Properties pane. Resize the page elements to match the tracing image.
I am trying to evaluate it. I imported the images and then opened the page template, but I do not see the Tracing Image list in the Properties pane in my Developer Org. The documentation does have:
Available for purchase in: Enterprise and Unlimited Editions
Available (with limitations) in: Developer Edition
However, it looks like it is completely unavailable in Developer Editions, making it difficult to evaluate.
Page Template's properties pane: