I have been working a lot in Scrivener to complete my thesis. I work on a mac and Scrivener is great, though there are some functions such as creating a Table of Contents which require a few more steps than working with Word for example.
First, select all the documents in the binder that you want to include in the ToC.
Next, goto Edit – Copy Special – Copy Documents as Toc.
Next, goto your ToC page in Scrivener and paste the Special Copy form the clipboard.
I work with Nisus writer Pro and the next step is after compiling your document as an .rtf in Scrivener, I open it in Nisus. The page numbers will not update just yet.
However, I found that if I waited a few moments, the page numbers updated themselves.
I hope this guide can be useful for others. Scrivener is a great app for writing academic papers and finding little tweaks like this are a great help.