You may want to go here, Penn State is all over accessibility- this links to a detailed up-to-date tutorial for users of InDesign 5.5+: http://accessibility.psu.edu/pdf/indesign/
It is preferable to perform the majority of the work necessary to properly structure and prepare a document for accessibility directly in InDesign, reducing the amount of remediation required. Below are basic steps that designers should take before converting files to PDF:
Keep text as “live text”, not as graphics or outline text which is not readable by a computer. Or if you must use place graphics instead of live text select the graphic and use Object export options to enter the actual text, which can then be read by a screen reader. Create PDF bookmarks too, whether you do it manually or with the table of contents feature.
Use paragraph styles consistently throughout your document. Consistent use of InDesign paragraph styles throughout a document is critical for efficiently and successfully exporting the content to PDF. Base styles on their hierarchical structure (main headline, secondary headings, subheading, and so on) and apply them appropriately to paragraphs according to their hierarchical role in the document.
Establish export tag relationships between InDesign styles and PDF tags. As you create InDesign styles, set each style’s Export Tagging (in the Paragraph Style Options dialog) according to its role in the PDF document— paragraph (P), heading levels 1 through 6 (H1–H6), or Artifact. Tables and bulleted and numbered lists are recognized automatically in the export process and tagged appropriately.
Anchor images within the content flow. Images in a print layout can appear anywhere in a spread, and sighted users can make the connection between the image and relevant text as they read. Screen readers process content in a linear fashion. Because screen readers use text-to-speech facilities to describe images, they should be placed as close as possible to the text that pertains to the image. InDesign’s drag-and-drop object anchoring makes it simple to place the reference to the image in an appropriate location without affecting the print layout.
Add alternative text for images. Screen readers can only indicate the presence of an image. Conveying what the image depicts requires providing alternative text (alt text). With the Object Export Options feature in InDesign, you can specify alt text from metadata in an image file or add custom alt text to any image, graphic or group of objects in a layout. Tag non-essential graphics as artifacts so they’ll be ignored by screen readers.
Incorporate internal document navigation mechanisms. In an accessible PDF, tables of contents, bookmarks, hyperlinks, and cross-references can act as navigation mechanisms to the referenced content. They also allow screen reader users to efficiently navigate the document by using the links these mechanisms create.
Establish content order in the Articles panel. The tagging order of a PDF document is essential to its readability. The Articles panel in InDesign CS6 enables you to precisely define which content in your document gets tagged and in what order. You can add content by dragging and dropping frames and objects into the Articles panel and then arranging them in the desired reading order. You can also break the content up into smaller articles without affecting the page layout.
Specify a document title and description as metadata. For accessibility, as well as for search engine optimization, a PDF file requires a document title and a description of its contents. When you save this information in the InDesign File Information dialog, it’s automatically transferred to Acrobat Pro X as required metadata.
Export as PDF with settings optimized for accessibility. When you use the InDesign PDF export options (print or interactive), the tagging, organizing, and bookmarking established in the layout become the tagging structure, order, and navigation scheme of the resulting PDF document.
Export for Accessibility
After you have prepared the document for accessibility in InDesign, you are ready to export it (File > Export) to PDF using the Adobe PDF (Interactive) or Adobe PDF (Print) format options. Which PDF type you choose depends upon whether or not your document contains interactive elements such as forms, buttons, audio, or video. Although the formatting is the same for both PDF types, they offer different options in their respective dialog boxes.. The Adobe PDF (Print) format exports bookmarks and hyperlinks but not buttons, audio, video, or animation. You can only opt to include the appearance of these interactive elements — not their functionality — or to not include them at all.
To be accessible, the exported PDF must be tagged, so make sure you select the Create Tagged PDF option in the Export dialog box for either PDF type. In the Export to Interactive PDF dialog, select the Use Structure for Tab Order option to save yourself that step in Acrobat later on. To activate bookmarking, hyperlinks, cross-references, and buttons, set the Forms and Media option to Include All. All other settings in the dialog are optional and subject to your specific needs or preferences.
Penn State has a great resource for accessibility best practices: http://accessibility.psu.edu/pdf/indesign/
Based on Adobe Document “Creating accessible PDF documents with Adobe® InDesign® CS6”
More on InDesign to PDF settings: http://help.adobe.com/en_US/indesign/cs/using/WSa285fff53dea4f8617383751001ea8cb3f-70c0a.html