It is always recommended to create GPO to disable automatic updates and let the software update patching happens through ConfigMgr.
Jason has written 2 blogs on GPO and software update management, please read the following. In case you have a local Group Policy setting that is configured with Microsoft update service location which will always be overwritten by an Active Directory Group Policy setting, and this can result in the Configuration Manager client failing to obtain software updates using Configuration Manager. The following snippet shows the local group policy setting for the client that is enabled with software update agent. The Group Policy setting used is the intranet Microsoft update service location, specified as a Windows Update computer administrative template. When a Configuration Manager client is installed and configured to use the software updates agent, it will automatically configured with a local Group Policy setting that specifies the Configuration Manager software update point.
