Hello there-
You can set up multiple cycles or "Installation and Restart" policies to help here. To do this, you can start by cloning the out of the box policy. You can do this by going to Settings > All Settings > Agents/Plug-ins > Software > Patch Management > Windows -- and then clone the Default Software Update Plug-In Policy.
You can specify your "reboot" settings in either the default policy or the the custom policy you create. In addition to your selection, you can specify your reboot handling within the Notification tab of those policies.