I would strongly recommend to start modelling with ModelMuse, going through all the tutorials/videos in the software homepage.
After trying several commercial interfaces, MODFLOW and others, I think this interface is probably the best you can find to learn how MODFLOW works down to the package level.
ModelMuse generates comments in the input files that are extremely useful to understand the whole MODFLOW structure.
Ideally, before using ModelMuse, reading the MODFLOW-2005 and MODFLOW-NWT manuals, to understand the discretization scheme and boundary conditions conceptualization and parameters, should give you a strong basis to work with the software. Then jump to MF-USG and MF6.
Regards
Javier