This process is a single thread running on each processor, which has the sole task of accounting for processor time when the system isn't processing other threads. In Task Manager, expect this process to account for the majority of processor time.
The system idle process uses all the CPU time that is not used by anything else. CPU time is like any other time; you can't not use it. If you do nothing, you're still using time: you are using time to do nothing.
If the system idle process is using 99% of the CPU, then your CPU is busy only 1% of the time. That's good, not bad.