As you can see from below information. below are the major difference between. QMC and QEMC
1. One of the major difference between QMC & QEMC is that you can manage multiple instances of qlikview server using QEMC , but not by using QMC & also there are several settings & configuration which is not possible from QMC like Active Directory setting,command center configuration, in the application.
changing the database for creating QVPR(like from xml to sqlserver) etc
2. QEMC is used when you are dealing with cluster of server and QMC when you are dealing with one instance of server.
3. QEMC have Publisher by which you can also apply section access
Also there were other difference as well you can find out form blogs.