You have to install it through the License Server, it should just be a text file on the license server that is read. Should be a path like below, just take out the old contents and add the new licenses then restart the License Manager or have it re-read the file.
If you load the VMware license Server Tools application on the VC server and click the Config Services tab it will tell you the License file location.
C:\Program Files\VMware\VMware License Server\vmware.lic
Chapter 3 of install guide...
http://www.vmware.com/pdf/vi3_installation_guide.pdf
