To set up Webmaster Tools, visit http://www.google.com/webmasters/tools and sign in with your Google account – preferably the same one you use for GA.
Click ‘Add a Site’. And enter your site’s URL.
Next, you’ll need to verify that the site is yours. You’ll be given a number of options, but the easiest way is to verify via your GA account.
For this to happen smoothly, you’ll need to be an administrator of the GA account (if you’ve only got ‘User’ permissions; ask the site’s Administrator to upgrade you).
That’s it. Your account should be authorized and ready to use. Though, when you’re setting up Webmaster Tools for the first time, it may take a few days for data to appear.