The 500-page Scrivener PDF manual is well-written and comprehensive. In this post, I've collected some of my favorite features in Scrivener with pdfoo URLs back to relevant section of the Scrivener manual for details.


The text below includes pdfoo:// URLs which will work correctly on your Mac after installing PDFoo and assigning the "scrivman" prefix to the Scrivener v2.3.1 PDF manual (5.0 MB). See the post on Taming PDFs with PDFoo and how to Build Mindmaps with PDFoo URLs for details.

1. Collect and organize Research for your writing project, including web pages, PDFs and media files. See scrivman/11 Gathering Material/. Attach a synopsis or notes to each research document using the Inspector pane to locate it easily using the Find Synopsis window. Scrivener documents are RTF-based and support pdfoo URLs, making it possible to directly link into any TOC or page of your PDF reference collection.
2. Record audio into your project, pick a research folder to store the audio file. Supports pause & continue recording. Can also use your Mac’s isight camera to capture a quick sketch/document. See   scrivman/21.4 Recording Audio and Photo Notes/. 
   
3. Break up the book Project into a nested tree of short documents, to be ultimately compiled into a book. Split up a long document into many for more organizing flexibility. See scrivman/15.3 Editing with Scrivener/. Use the Scrivenings mode to combine several short documents into one long document temporarily for fluid editing. See scrivman/15.8 Editing Multiple Documents/.
   
4. Assign custom labels, keywords and status flags to your documents, which show up in an elegant visual layout in the Corkboard view. Labels and keywords show up as colored adornments on index cards. See scrivman/10.1 Meta-Data Types/. 
   
5. Connect relevant research materials to your document using the References pane in the Inspector. Scrivener also makes it possible to see all documents that refer to a particular research using backlinks. See scrivman/19.3 Document Support Panes/. 
   
6. Use the Find Synposis window (shortcut CTRL CMD G) to search and open up handy Quick Reference panels to support your writing. See scrivman/21.1 Searching and Replacing/. Use the Inspector pane to add/edit synposis for your documents and research to ensure the Find Synposis command works. See scrivman/19.1 Synopsis Card/.
   
7. Set up the Split editor for reviewing research materials while you write, and learn the keyboard shortcuts to control the contents of the inactive editor while you write. See scrivman/14.4 Splitting the Editor/.
   
8. Use colorful inline annotations in your document to serve as comments on specific parts of your document. See scrivman/18.1 Inline Notation/. These inline annotations can be exported as “margin comments” when compiling your project to .doc format for further processing. See scrivman/24.20 Footnotes/Comments/.
   
9. For books that require working with images, tables, and extensive cross-referencing, it is best to finish up editing in Microsoft Word or Apple Pages. Use the .doc compile format to export the book from Scrivener and import into Microsoft Word or Apple Pages. See scrivman/24.3 Available Compile Formats/.
   
10. Track progress on the entire project in terms of total words, or set targets for each writing session or document(s). See scrivman/21.3 Goals and Statistics Tracking Tools/.
    

Workflow for annotating PDFs
Skim.app is a free, open source Mac OS X app which is great for annotating PDFs. In particular, the Text Note tool provided by Skim (shortcut CTRL CMD 1) allows you to draw "sticky notes" on a PDF page and write comments. Skim does not modify the original PDF directly, and annotations are kept in extended attributes, i.e. hidden information attached to the PDF file on disk. To ensure that these annotations do not get clobbered when syncing PDFs via Dropbox or a similar application, make sure to turn on "Automatically save Skim notes backups" option in Skim Preferences. This will create a small-sized .skim file adjacent to the original PDF to hold all the Skim-created annotations. This is a reliable way to annotate a PDF on multiple computers using Skim, since only the small-sized .skim file has to be synced across computers.

Export PDF Annotations with PDFoo
Skim can export a new PDF with embedded notes (i.e. annotations) using the File > Export menu command. Open this new PDF using PDFoo, and export annotations with pdfoo:// URLs that provide a context for each note and allow you to jump back to the source PDF.

Dictate Note Annotations
The voice dictation feature in Mountain Lion opens up the possibility of quickly adding note annotations to a PDF. To add a text note annotation to a PDF opened in Preview.app, use the Tools menu > Annotate > Note command. Use the voice dictation feature (shortcut fn fn) in 10.8 to dictate the note. Continue adding note annotations to the PDF, and use File > Save a Version (CMD S) to embed the notes into the original PDF.

Export PDF Annotations with PDFoo
Next, open the PDF in PDFoo, assign a prefix, and export the PDF annotations to a text file. Each note will be followed by a pdfoo:// URL which links back to the original PDF. Follow the link to lookup the context for your note. Save your exported notes in Evernote/Scrivener/DEVONthink for easy search and retrieval, or share it with your colleagues via email or the web.

Like to Dictate? Get Dragon Dictate
OS X 10.8's inbuilt voice dictation feature has a few shortcomings currently: it has to connect to Apple servers for processing which introduces a noticeable lag, it doesn't quite work well with accents, and it requires keyboard intervention to switch it on and off repeatedly. For users who find the dictation feature useful, Dragon Dictate for Mac v2.5 (currently $80 on amazon) is a worthwhile upgrade which addresses the above limitations.

Why export PDF annotations? 
Do you read and refer to important PDF documents at work? Do you make notes and annotations using tools like Preview.app on Mac OS X and iAnnotate or GoodReader on iPad? Are your insightful notes locked away in the PDF? Would you like to make your notes accessible and easily searchable? PDFoo enables you to export notes and comments from these PDFs into text to share easily with your colleagues, or to index and search inside your favorite note-taking application. PDF annotations are largely useless without context however. Using PDFoo app, you can easily attach pdfoo:// URLs to each text annotation, and the context for each note is just a click away.

Workflow Guide
PDFoo can export notes and highlight annotations from your PDF to a text file (RTF format). Further, it inserts pdfoo:// URLs to link back to the location for each note in the original PDF. Simply follow the pdfoo URL to open up the PDF and view the context for the annotation. The workflow is as follows:

1. Use Preview.app or any other PDF annotation tool to create text, note and highlight annotations in your PDF.
2. Open up the PDF in PDFoo via File > Open... command
3. Assign a Prefix to the PDF via PDF menu > Set Prefix... command, or the toolbar button, or CMD-L shortcut. This prefix will be used in generating pdfoo:// URLs.
4. Use File menu > Export PDF Annotations... command, or Opt-CMD-A shortcut
5. PDFoo generates a RTF text file with the text of annotations together with pdfoo:// links. Save the contents via copy-paste into Evernote, DEVONthink Pro Office, or any other rich-text compatible application. Clicking on any of the pdfoo:// URls will open up the original PDF to the correct location.

More about PDFoo
Watch the PDFoo Quick Guide video, or skim the PDFoo overview document, or download and try out "PDFoo Lite", and purchase the unrestricted version of PDFoo on the Mac App Store.

PDFoo enables linking into PDF content. The concept has a simple analogy: to link to web pages we use http:// URLs. Similarly, to link to PDFs we can use pdfoo:// URLs. These PDFs reside on your computer, and PDFoo resolves the URL to figure out which PDF to open. For example, PDFoo is wired to respond to pdfoo://apphelp/ URL to open the PDFoo help document.

Creating PDFoo URLs is easy: First, open the PDF. Second, assign a prefix such as "motion5man" for 1500-page Motion 5 PDF Manual. Third, drag out links to sections inside the PDF, or copy out specific paragraphs with links back to source, or even export annotations with links back to the original PDF.