I found the solution myself.
But, this solution works on Windows 2012 Server with IIS 8.0 or Above and Pleask control Panel with SNI Support. To read about SNI, just google. We were using Virtual Private Server. So i have had control over every setting in the server.
Follow the steps described here.
But it doesn't mention about Setting up SSL properly. So follow the steps below after completing instructions given in above post.
With IIS 8.0 you can create different bindings for each domain with each domain having its own certificate. You have to use SNI, which means very old browsers (eg. IE6) won't work as they don't support SNI. but that is not a huge concern I think, especially as WinXP is already out of support. Most browsers even on mobile platforms now support SNI.
More info here and a great walk through is here. Not for the faint-hearted!
I would also advise (if you are on dedicated server) using Central Certificate Store to manage the SSL certs - so much easier once you understand it than the old way!
But note, this WILL not work with this combination of browser and OS. And also by the way on nop commerce multi-store set up, all of your emails for domain alias works as email alias too.