The bookmarks list on the left hand side of the Versions main window contains all repositories and working copies that you have bookmarked. See the Getting started section for instructions on how to add new bookmarks.
The small badges next to working copy bookmark show how many items have changes. A blue badge indicates changes in the remote repository, while the yellow badge indicates local changes in your working copy.
Versions automatically places new working copy bookmarks under the correct repository and adds a repository bookmark for a working copy if necessary. To organize them further, you can group a set of bookmarks into a single folder. You can do this by selecting “New Bookmarks Folder” from the “Bookmarks” menu, then dragging any bookmarks or other folders into the folder you just created.
To rename a folder, select the folder in the bookmarks list, then click on the name of the folder again. You can also control+click the folder and choose “Rename Folder...” in the contextual menu that appears.
When you delete a bookmarks folder, every bookmark in it will be deleted too. To remove the folder and keep its contents, control+click the folder and select “Ungroup” from the contextual menu. To make this a bit easier, Versions presents you with the option to ungroup a folder instead of deleting it when you try to delete a folder that contains any bookmarks or sub-folders.
If you use a single repository for multiple projects, it's still possible to organize your bookmarks by project. Add one bookmark for the top level of your repository and several more repository bookmarks under it, each with a URL that points to a sub-folder in the repository. If your repository requires authentication, you will only need to enter your username and password once.
With a setup of nested repository bookmarks, the Timeline for each bookmark will only contain items that are relevant to each bookmark's sub-folder in the repository.