Most synch programs use the file stamp to determine which is newer and which is older. Some synch programs offer options on this as well, but generally speaking, the more recent file will overwrite the less recent file.
Originally Posted by Dan Phillips
IOW, the file that was saved last will overwrite the file that was saved earlier than it.
Thus, when you synch between laptop/desktop, the synch program will automatically replace the older files with the newer ones, regardless of which computer they are on.
For example, if you updated the notes in Romans 1:1 on your desktop, then went over to your laptop and updated the notes in Galatians 1:1, when you synch the two, each of the newer files will be placed respectively on the laptop/desktop.