Hi Nikuni, You'll need to login to the analytics profile that you like to link to webmaster tools. Then, click admin and navigate to the property setting tab, at the bottom of the page you'll find a link "edit", click on it and choose the right webmaster tools profile to link it to. Hope this helps.
If someone noticed, there is a very big gap in google webmaster data and data showing in google analytics search engine section (where we linked webmastertools). I don't know why.
Yes.. I do agree with you.. There are many difference in numbers when you match the webmaster tools data with Google Analytics data on "Search Engine Optimization" section. Even i have no idea why its happening so.. Any way one thing for sure, Google Analytics wont provide full details from webmaster tools. So its always better to pull data from webmaster tools itself when it comes to CTR, Impressions etc...