Jetpack currently uses a sun/moon strategy where the current production files are in one folder and the "staging/test" version are in the other folder.
If you don't want to keep track of which folder is in use during development, you can update your Unison preference file to point to wp-content/mu-plugins/jetpack-plugin/production on your sandbox. The production directory will always be pointed at the current production files.
In the event that you want to sync changes to both sun and moon, you may want to create two Unison preference files, one file which syncs to the sun ___location and one file which syncs to the moon ___location. Then you would run two separate instances of unison watch (as described above).
For even more advanced usage, you can use the following command to launch tmux with each unison command running in a separate window.
tmux new-session -d 'unison -ui text -repeat watch jetpack-plugin-moon' \; split-window -d 'unison -ui text -repeat watch jetpack-plugin-sun' \; attach
Note: You will need to adjust the above command depending on the name(s) of your Unison configuration files.