For changing the settings of eve you have to go in mugen1 folder, for the main settings you have to modify mugen.cfg file with a text editor.
But there are even other files like system.def and fight.def,
every .def and .cfg file, controls an aspect of the game.
A quicker way to edit the select screen is using a program known as Vselect, that gives you the possibility to move the characters cells, and edit with a graphic layout without coding, but before you must give to the program the path of where you have installed your mugen, so you have to tell him where the mugen.exe is located.
The mugen main settings, like resolution, video settings and performance settings, are inside : mugen.cfg
the screenpack main settings are inside : System.def
The characters selection screen settings are inside : Select.def
you can find in the description the Vselect download link (the program for modify select.def without coding).