When you try to enroll a new certificate using the AD CS Web Enrollment point you are unable to select the custom AD CS template you would like to use.
When the custom template is being created click on the Subject Name tab and ensure Supply in the Request is selected. This is a must if you are creating certificate for non domain-joined devices like network appliances.
Click on the Security tab and add the Web Enrollment server computer object to the ACL and ensure it has Full Control permissions.
Ensure you issue the certificate template to AD.
Go back to the web enrollment point and you should have the option to use this new template. Please note you might have to force AD replication.