The EEGLAB plugin for microstates is mostly documented in the help of the different functions of the plugins.

To get a basic overview of the procedures, you may also call:

help_HowToDoMicrostateAnalyses in Matlab

There is also a Matlab script in the package called TestMSAnalyses.m that performes an entire microstate analysis with two groups of subjects.

Finally, here's a brief video that guides thru a standard analysis and explains the underlying concepts.

Download / view the video