I signed up the trail for GSM, and getting expired in 90 days, How to get a permanent GSM user and confi

I think that from the Commerce Portal (where you signed up for the trial) you can also claim your Software Assurance benefit to convert your trial into a permanent license.

Terms and conditions for GSM as a software assurance benefit - http://technet.microsoft.com/en-us/library/jj984239.aspx

I'm stuck on how to convert to Permanenet with Software Assurance benefit? Further will it work on 2012 R2 right?

Where are you stuck? Just go back to the Commerce Portal where you signed up for the trial and it should allow you to claim the SA benefits. I can't check how it looks like once logged in, but I see from this page there are both links for 'trial' and for upgrading for 'full service' http://www.microsoft.com/en-us/server-cloud/system-center/global-service-monitor.aspx

Yes it's both for SP1 and R2.