How can I takeout JBoss headers completely (I just need to see my website)?
You may need to set up your page with "Show Max Window".
How can I change the left and right margin of default page (Which files need to change)?
You may need to define a new skin or modify the default one to make your portal CSS suitable to your need. To modify the default skin, it's hard to say what exactly are needed to be changed as It much depends on your need. BUT you could run portal in debug mode and try to use Firebug to see which CSS you want to change.