I just updated to 9.0.4.0 and was concerned that they'd removed the ability to set the default output type for a DVD to "DVD Folder" or removed the ability to set a default location for output and/or temp files. It isn't in the most obvious place in the settings, but it is still there.
- Open up settings (the little gear/cog icon along the top of the main app view).
- In the "General" item under the "General" tab, fill in the "Output Directory" and "Temporary Directory" you'd like.
- In the "DVD Copy" item under the "DVD" tab, select the "Default output type" you'd like.
That should be all you need to do so that next time you start DVDFab it defaults to write the output where you want them.