When doing an upgrade you should always run setup of the new operating system from with in the old system. In other words you boot up your old Win 98 system that is currently on the CPU hard drive, and after Win98 is fully up and running then pop in the Win 2000 pro disk and run setup from there. Now there is memory and processor issues when attempting to install Win 2000, or XP, you must have at least a minimum size, or amount of Ram, processor and harddrive space. The setup documentation will explain the minimums required.
Mike