lgunda,
You can right click a running server in the Servers view and open the admin console to set some properties there.
We also have properties on the MyEclipse EAR property page (for EAR projects) – where you can specify a few deployment options.
Other than that, the preferences that you see when configuring the sever and profile are what we have – are you interested in any preferences specifically? We can take a look at including them in the next version of MyEclipse.