I believe I understand. So reboot can happen at any time but only after computer is idle for an hour for instance.
The reboot options within ITMS Patch Management allow you to reboot right after a patching cycle competes or at a certain time which doesn't sound like it meets your needs. Also, the Altiris server doesn't know when a machine is idle so you won't be able to do this with a task without combining some client-side logic.
If it were me, I would create a custom script that checks if a reboot is pending and reboots the machine. Then instead of running that as a Altiris task or policy, run that script as a scheduled task using Windows scheduler. Scheduled tasks have lots of options to use as triggers, one of which is how long a system has been idle. So you could schedule the reboot task to run every 30 minutes but only when the system has been idle for an hour. The task won't do anything unless a reboot is required.
If the patches you are installing are for custom software that doesn't set the system reboot required registry flag, you could use a custom registry key as a reboot flag and make sure your script flips the flag when it reboots. Then your custom packages could set the flag whenever a reboot is needed.
SchTasks.exe is a command line tool that can be used to schedule a task or there are VBS objects and PowerShell methods as well. You may find it easiest to setup the task the way you want then export it and use a command line to import the configured task.
Info on determining if reboot is required including a PowerShell method:
http://blogs.technet.com/b/heyscriptingguy/archive/2013/06/10/determine-pending-reboot-status-powershell-style-part-1.aspx