Which Scrivener template should I use for a Cornell dissertation or thesis?
Avoid the non-fiction essay templates which lack chapters and thus will cause problems when you compile.
Choose either blank or non-fiction -->general non-fiction template which allows parts, sections, and chapters. (If you started writing a thesis or a dissertation using one of the essay templates, create a new non-fiction project and drag and drop the documents into it.)
How should I set up Scrivener for writing a dissertation or thesis?
Tips from Hacking the Thesis at The Ohio State University
Can Scrivener create a Table of Contents?
Yes. All Scrivener projects have tables of contents.
But for academic writers, make sure you've chosen a template that allows chapters.
Use "Edit ▸ Copy Special ▸ Copy Documents as ToC" and paste it into the Scrivener document.
When you compile as a PDF, the ToC will be formatted text, but if you compile into Word, the ToC will look like hyperlinks. In Word, copy the ToC and "paste special --> unformatted text." Adjust formatting in Word to suit.
Not specific to a academic writing but nonetheless useful: step by step directions on Table of Contents from Scrivener Virgin
How do I format a dissertation in Scrivener?
Scrivener was designed for fiction, not dissertations. It can do a lot, but it might not be able to do everything if the dissertation requires complex formatting. In such cases, plan to use Word as a last step. When you're ready to submit, compile the dissertation into Word for a final round of formatting and use the Cornell Graduate School's Word templates for dissertations
Not specific to a academic writing but nonetheless useful: step by step layout & compiling tips from Scrivener Virgin
What cloud storage is recommended for Scrivener?
Because a Scrivener project consists of lots of parts, all cloud storage services have the potential for error when syncing Scrivener projects. Scrivener recommends saving the backup to Cloud Storage, not the original. More info
Scrivener leans a bit towards Dropbox; the mobile Scrivener app has been designed to work with Dropbox. Dropbox is freemium. If you're not a Dropbox user, consider using it for Scrivener and only Scrivener. Other Cloud services (such as Google Drive, Box, OneDrive,etc.) can be used but have the potential for errors.
Can I use Zotero with Scrivener?
Yes, but understand that Zotero isn't as fully functional with Scrivener as it is with Word and Google Docs. However workarounds exist.
How to Use Zotero and Scrivener for Research -Driven Writing from Daily JStor has tips for incorporating Zotero notes and annotations into Scrivener.
Can I use EndNote with Scrivener?
Yes, but it's not as seamless as Word.
Instructions: Copy a reference from an EndNote Library and paste it into Scrivener which will be a temporary citation. Compile the Scrivener project into Word. Open the document and choose “Update Citations and Bibliography” button OR compile to an .rtf file, then in Endnote, go to the tools window and choose “Format Paper.”
What about Scrivener and foreign languages?
Change the interface language under "Preferences/Options -> Language."
Add diacritics under "Preferences/Options -> customize shortcuts."
Additional tips for working with non-Roman characters (from the Scrivener forum)
Can I install Scrivener on multiple computers as well as mobile devices?
Yes, the license allows up to five, if the computers are the same operating system. PCs and Mac's require different versions of Scrivener.
Mobile Scrivener for iPhone and iPad must be purchased separately. Best practice is to share the Cloud-stored backup version of a project between computers, not the original.
Can I collaborate with Scrivener?
Scrivener was designed for drafting, not collaborating, but Scrivener projects can be shared if all parties have Scrivener. Share a project via email as an attachment. Under Options is a "Sharing" feature that allows import and export of projects. Alternatively, compile for Word and share the Word document. A Word document imported into Scrivener will not retain its Scrivener "track changes" features.
More questions?
Consult the Scrivener User's Manual or the Literature & Latte Scrivener forums.