Just change your process to "cd" to the directory where s3sync.rb (and I assume s3config.yml) is installed at.  For example:

cd /root/s3sync && /usr/bin/ruby ./s3sync.rb -r --ssl /my_dir_to_backup bucket:pre

Since you're fully qualifying the path to backup, the location the script runs from doesn't matter for the process, so this just starts it out in the "installed" directory.

- Jon