To MDM capabilities of iOS you need to get MDM certificate using your Enterprise developer account.The generated APNS certificate for MDM will be used as MDM certificate.You can get more details in third party MDM vendors site about how to generate MDM certificate. For example you can go through mcafee site or follow the below steps.
1)Follow MDM_Protocol pdf .
2)Follow this page: http://www.softhinker.com/in-the-news/iosmdmvendorcsrsigning
Then verify few things.
remove the passphrase from customerPrivateKey.pem using this command
openssl rsa -in customerPrivateKey.pem -out PlainKey.pem
Then merge your APNS certificate (for example CustomerCompanyName.pem) downloaded from the portal https://identity.apple.com/pushcert/ using this command
cat CustomerCompanyName.pem PlainKey.pem > PlainCert.pem
Now this PlainCert.pem file can be used in your server as APNS/MDM certificate.
3)For MDM config profile use IPCU and look in to this also.