Any changes to those files are not going to persist when you reboot the
machine. The /sys directory is populated/refreshed by the kernel during boot,
to provide info about the underlying hardware to userspace processes.
I was going to suggest adding some commands to one of the init scripts, so
that the fans are set to max automatically when the machine boots up. But,
Magic Banana's suggestion to create some scripts that you can easily run
should work as well.
As I said before, a better solution than just maxing the fans would be to
either fix the applesmc module or make a daemon process, but those are a lot
more involved.
