The Linux software clock is not always accurate. It is kept running by a periodic timer interrupt generated by PC hardware. If the system has too many processes running, it may take too long to service the timer interrupt, and the software clock starts slipping behind. The hardware clock runs independently and is usually more accurate. If you boot your computer often (as is the case for most systems that aren't servers), it will usually keep fairly accurate time.
If you need to adjust the hardware clock, it is usually simplest to reboot, go into the BIOS setup screen, and do it from there. This avoids all trouble that changing system time might cause. If doing it via BIOS is not an option, set the new time with date and clock (in that order), but be prepared to reboot, if some part of the system starts acting funny.
Another method would be to use either hwclock -w or hwclock --systohc to sync the hardware clock to the software clock. If you want to sync your software clock to your hardware clock then you would use hwclock -s or hwclock --hwtosys. For more information on this command read man hwclock.