Hi Siva,
As per my understanding installing any new license will overwrite the existing CMS.lic file, you can contact the licensing team to provide you a consolidated file that covers all the licenses that you have purchased.
As far as PMP/SMP license assignment to users is concerned it is covered on page 12 of the following link
http://www.cisco.com/c/dam/en/us/td/docs/conferencing/ciscoMeetingServer/Deployment_Guide/Version-2-1/Cisco-Meeting-Server-2-1-Single-Combined-Server-Deployment.pdf
HTH
Manish