To save the configuration:
6509# wr    (press enter)

To reboot the switch:
6509# reload    (press enter)
Proceed with reload? [confirm]    (press enter)

To shut down the switch:
Turn off the switch on the Power Supply Unit of the switch.

But remember one thing, if your switch is acting as a NTP Server as well, you may want to make sure that the time settings are done once the switch is restarted as it does not keep a track of the time and it gets reset.