How to set the NTP server used by Windows Server 2008?
Go to Start menu, set the time and date in section Clock, Language, and Region, Internet Time tab, Change settings and put your ntp server in the Server field.
Depends on why you're doing this. If you're talking about a standalone server, follow the steps given in the other answers. If you're in an AD environment, be aware that only the DC which holds the PDC emulator role should have an NTP server explicitly set; every other server (and client) should not have an NTP server set - at all. This is required so that the correct domain-based NTP hierarchy will take effect.
This is why we need more info - we may be able to give you the correct answer to your specific question, but whether the answer is correct or dangerous for your environment will depend on your environment, and only you can tell us that.
w32tm /config /manualpeerlist:<time server to use>
may do what you're asking.