I'm trying to map the site structure we have created for a SharePoint 2007 site- is there any way to do this automatically compared to manually?

What kind of site structure you want to make...can you explain me moreCheers, Hemendra-MCTS

We want to show how the folder, page and site structure has been designed and we'll then annotate it with our rationale for these decisions.

There is no automated way for it. If you designed the structure of site and want to create duplicate site on same server or different server then you can only create a Site Template for that. Cheers, Hemendra-MCTS