The best way to get started using FieldTrip is by reading through the tutorial documentation and through the other documentation.
FieldTrip is a toolbox containing separate (high-level) functions, not a program with a graphical user interface. The toolbox functions can be combine into an analysis protocol, i.e. a Matlab script containing all steps of your analysis.
FieldTrip has a generic mechanism for reading data from file. Within FieldTrip there is no difference how the data from one file format is treated, compared to another file format. Many EEG, MEG and electrophysiology file formats are supported. There is a small difference between EEG and MEG data, because in MEG data the sensor positions are explicitely represented in the data. Therefore in case of MEG data the sensor information is kept with the data, all combined in the FieldTrip data structure. For animal electrophysiology data there is also a difference in the representation of local field potentials (c.f. EEG) and in spike timestamps and spike waveforms. Although FieldTrip represents all data in a similar way, for some acquisition systems and/or file formats it may help if you understand how the peculiarities of that file format are related to the FieldTrip implementation.