Yes, cp -rp /path/to/site /path/to/backup_dir will work, but its better to use:
cp -Rp, it is a safer version of the command.
Also, VERY IMPORTANT, this will only backup your files -- most likely you have a database associated with the site which will need to be backed up as well:
mysqldump -Q -q -e --add-drop-table --database DATABASE_NAME > DATABASE_NAME.sql
Replace DATABASE_NAME with your db and this will make a file with all of your SQL data, best thing would be to run this command in /path/to/backup_dir so you have all of your restore files in 1 place.
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