You can turn off automatic updates if you're going to be doing something.
If you've already installed the updates, and are being hassled about a reboot that you're not ready to do:
Start > Run > services.msc
Find the Automatic Updates or Windows Update service and stop it.
Now, you do need to perform updates, and you do need to reboot before the update is finished, but this will keep you from having to sit over the computer for 9 hours clicking "Remind me later" while you're waiting for your job to finish. Just reboot when you're ready.
Microsoft almost exclusively releases their updates on the second Tuesday of each month. If you want to get them out of the way before a long operation, you can use the Windows Update shortcut (under XP) or the Windows Update Control Panel (Vista, 7) to check for updates and apply before rebooting and running the long operation.
