You need to use mysqladmin to set the root password for the first time. Assuming my password here is bobby:
mysqladmin -u root password bobby
And can we have two mysql instances in a machine(mysql of wamp and individual mysql component) ?
Yup - but they'll need to be separate installations, using separate sockets and run on separate ports. It's possible but not what's generally done - the norm is to use the same install and just have separate databases with separate users (each user only having permissions for each database.) Beyond that there's not a whole lot of need for separate installations on the same server.