Yes, the files will reside on the desktop, with synched copies on the laptop - if that's the way you want it, but there's nothing to stop you setting up the briefcases the other way around (files on the laptop, briefcase on the desktop)
Updating the briefcase synchronises in both directions - it copies updated file on the desktop to the laptop, and updated files on the laptop back to the desktop.
The only problem occurs if you've updated a file on both machines, but you'll get given the option of what to do in that case.
Hope this help,
AndyF