lammert - 6:44 am on Jul 16, 2010 (gmt 0)
Hi pradeepkhutale, first of all Welcome to WebmasterWorld!
There shouldn't be any negative effect of adding both domains to GWT. Adding both and using the option "Display URLs as ..." is an extra signal to Google that both domain names are in effect pointing to the same content and one of those is the preferred display version. It may help to prevent erroneous behavior while indexing your site.
I would leave the situation as it is now.