What is preferred domain settings in Google Webmaster tool

I had done adding my site to Google Webmaster tool. I am getting certain messages in that for settings up a preferred domain. When I go in the settings I found two domains. There is one with www and other one without it. I want to know that how to fix this settings. And if I ignore this then will it cause any problem. I am not able to completely understand this thing and it is very complicated to fix also. i am getting the message all the time. I just want to get rid of this thing but it is not working at all. I had tried chatting with some of my friends who still are not aware about this thing.

Well if you are getting this message the better fix it. Here Google identify two url of your site. One with www and other one without that. So there are chances of having a lot of duplicate things indexed on your site which can create ranking issue. So the best thing is to fix it by. Just go in the settings and then simply select a preferred domain. Do not forget to add a permanent 301 redirect in htaccess so that you wont face much problem with the links you had already generated. For a new site there is nothing much to worry.

Agree with aadidev i would suggest the same.

There is one thing you have to take care while doing the same. It is necessary to setup a htaccess redirect here. Then you have to re-verify the domain back again. If you are using a non www version then you will have to use the same kind of HTML verification file that you had used before and verify the site in the web masters tool. I am quiet sure that this will really help you in fixing the problem. And it might start working well also. If you are confused about using the same then ask question on the Google product forum about the same. You will get a more appropriate guidance on the same.