Linux provides the stime(2) call to set the system time. However, while this will update the system\'s time, it does not set the BIOS hardware clock to match the new system
I would also like to point out the hardware clock is only accurate to a point (I have seen systems that will loose/gain a couple of seconds a day).
Have you considered setting up the network time daemon to sync your clock against a time server?
Admittedly this syncing does not happen until after the daemon starts so keeping your hardware clock in sync also helps between the power up and the point the time daemon syncs against the time server.