There are many ways to do this:
1) From AccessPoint
2) From QlikView Developer "Open in Server"
3) From QMC
If you want to allocate this using the QMC on the server, you should be able to use the following to get to the QMC screen:
The above assumes that you have a normal QlikView server deployment and also you're in the QlikView Admin group on the server as well.
From here you can go to the system tab, click licences, select Qliview server from Type, in the righthand window you should then get Client Access Licences (CALs) as a tab, click on this then Assigned CALs under this. From here you can see manage users icon (looks like two small people) on the top right of the name grey bar, click this and then allocate the CAL manually by adding the user accordingly.
I am also assuming you mean a named user CAL? Document CALs are managed in a different place.
Hope this is helpful.