Ideally you would have updates set to run during times when the PC is not being used such as late at night or early in the morning. If your computers have hardware that allow Wake-On-LAN to function, you can schedule a Wake-On-LAN action from the Power Save Console a few minutes before the updates take place.
Generally the default disk and processor thresholds should be sufficent to prevent a workstation performing updates from going back into a sleep state.
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