Earlier today a designer asked me for help creating a PDF with two different depths of tables of contents. He said, "I'm creating a PDF manual in InDesign. The Table of Contents [on the page] needs to list only Chapter Title and Heading 1 [paragraph styles], but I want the navigational menu [Bookmarks sidebar] in the PDF to list Chapter Title, Heading 1, Heading 2, and Heading 3 [paragraph styles]."
That's easy. Here's how.
1. Create the on-the-page Table of Contents and uncheck the option to Create PDF Bookmarks as in Figure 1.
Figure 1: Creating the first, on-the-page table of contents.
2. Also using the Layout > Table of Contents command, set up the second, deeper TOC for the Bookmarks sidebar. In this version, do check the option to Create PDF Bookmarks. Also ensure that Replace Existing Table of Contents is disabled.
3. Place this table of contents on the pasteboard, not on a page, and not overlapping or touching any page (see Figure 2).
Figure 2: Creating the second TOC to become PDF bookmarks.
4. Export to Interactive PDF and enjoy the two TOCs (see Figure 3).
Figure 3: The resulting PDF with both tables of contents—the smaller, on-the-page version as well as the deeper Bookmarks sidebar.
Reprinted from http://iampariah.com/blog/creative-pro/indesign-pdf-creating-separate-tocs-bookmarks-page. php by the author.