The section towards the end of the Configuring the Documentation Theme page in our Confluence 4.0 documentation more or less covers this.
To do what you want, when you configure the Documentation Theme for your Confluence space, clear the Page Tree check box but instead, add a Confluence Page Tree Macro (for your TOC/navigation tree) in the Navigation text box.
That way, you can add other content above the Page Tree Macro so that your TOC/navigation tree isn't the first thing that appears at the top of the left-hand navigation column.
Hope this helps.
P.S. While wiki markup was removed from the Confluence 4.0 page/blog editor (because from Confluence 4.0, page/blog content is stored as XHTML - not wiki markup), wiki markup is still used when configuring the Documentation Theme in Confluence 4.0 and later. For details on using wiki markup, please consult the Confluence 3.5 Documentation.
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