Just connect to DM after you're done with the upgrade to start EA. When you do the upgrade you can also run Loader.exe from a command prompt and add the switch /provision and it will EA (if you're connected to the mail server properly.)

Personally, I just do the OS upgrade, then I check out a few things then plug in to DM to start EA when I'm satisfied the OS is working ok. I hate to EA only to find an issue with the OS and then downgrade and have to EA again.