I am just starting with Java EE6. i have installed netbeans 7.2 though the sample applications based on java EE6 runs successfully. My question is do i still need to install Java EE6 SDK?? if not, then why is that Java EE6 SDK comes separately???
No you don't need it.
Java EE SDK is available as a standalone package because SUN's philosophy was not to require any specific environment (IDE) to do Java development.