Starting with Scrivener 2.0, you can sync projects with Index Card. This includes the title, synopsis, and order of cards in your project. If you are using Scrivener 2.2 or later, you will find that the main text of Scrivener will now sync to the long text field of Index Card, instead of using the notes field.
The folks at Literature & Latte have put together a fantastic video on how to sync Scrivener with Index Card for iPad or iPhone. You can also find printed instructions in the Index Card for iOS section of the Scrivener User Manual.
Index Card 4 adds the ability to export your Index Card projects as a .scriv Scrivener file. This will maintain stacked cards, and formatting you've done to body text. Note this is a one-way Index Card iPad to Scrivener desktop trip. It should work for Scrivener on both Mac and Windows.