To apply a license file to a multi-tenant controller, copy the license file to the controller home directory for the same user who has installed the controller.
Check the expiration date from license.lic or in readable format using http://www.ruddwire.com/handy-code/date-to-millisecond-calculators/#.WI7a87Z96gT
Log in to http://controller:port/controller/admin.jsp as the root user.
Select the relevant account and update the expiration date and license units per the license.lic file.
Finally, logout from the controller and login to http://controller:port/controller/ as the admin user. Check the license screen to see whether the changes have been reflected successfully.
These steps are for multi-tenant env where admin has to distribute license units through admin.jsp page after dropping the license.lic file at controller installed directory /controller/.
You just need to drop license.lic file at /controller/ location and controller will read this file automatically.
Ref https://docs.appdynamics.com/display/PRO44/Applying+or+Updating+a+License+File for more details.