How to manage security policies on servers onboarded to Microsoft Defender for Endpoint using Azure

There are multiple ways of approaching this. If you onboarded the devices using Configuration manager then you can manage the Defender policies using Configuration Manager itself. Also, if it just the AV component that you need to manage, you don't really need Defender for Endpoint for it, although it is recommended in absence of a 3rd party XDR solution. You also have the option to Co-manage endpoints and cloud attach servers to apply the policies using Intune. Alternatively, you can use security configuration management feature within in Defender and enable the connector with Intune and apply the policies using Intune. Look me up if you need anymore assistance.