Windows Defender detects and removes known spyware only. It is not designed to protect against the full breadth of malicious software, and specifically does not prevent viruses, worms, Trojans, and other malicious software from infecting your machine.
Microsoft Security Essentials will not replace Windows Defender , but if you are running Microsoft Security Essentials, you do not need to run Windows Defender.Currently Microsoft Security Essentials does not disable Windows Defender, but it should and will in a later version of the beta.
You can safely leave both applications enabled. Do not need to manually disable Windows Defender .There are 2 processes by MSE which is MsMpEng.exe and msseces.exe. With Windows Defender you are realizing that the almost same services running so in the long run MSE will disable Windows Defender.