There are a few different ways to apply the Windows 10/11 Enterprise license that you have obtained through your M365 E3 subscription to your on-prem domain-joined computers:
Using the Volume Licensing Service Center (VLSC): The VLSC is a web-based portal that allows you to manage your volume licensing agreements and product keys. You can use the VLSC to download the installation media for Windows 10/11 Enterprise and obtain the product key for your subscription. Once you have the product key, you can use it to activate the operating system on your on-prem domain-joined computers.
Using the Key Management Service (KMS): KMS is a volume activation method that allows you to activate Windows and other Microsoft products within your organization without having to connect to Microsoft's activation servers. You can configure a KMS host on your network and use it to activate your on-prem domain-joined computers.
Using the Azure Active Directory (AAD) Domain Services (AAD DS): The AAD DS allows you to use your Azure AD tenant as a managed domain services solution for your on-premises environment. With AAD DS, you can join your on-premises Windows 10/11 Enterprise computers to the Azure AD tenant and use your M365 E3 subscription to activate the operating system on those computers.
Using Microsoft Endpoint Manager (MEM): MEM is a cloud-based management solution that allows you to manage and secure your Windows and macOS devices. You can use the MEM to manage the Windows 10/11 Enterprise license on your on-prem domain-joined computers.
It's important to keep in mind that, with all the above options, your computers must be domain joined to your on-prem AD domain, and the domain should be synced with Azure AD.
It's also worth noting that you should check the licensing terms before using any of the above options to ensure that you are using the licenses in compliance with the terms of your subscription.