Ediff has a rather self-explanatory interface, and in most cases you won’t need to change anything. However, should the need arise, there are extensive facilities for changing the default behavior.
Most of the customization can be done by setting various variables in the .emacs file. Some customization (mostly window-related customization and faces) can be done by putting appropriate lines in .Xdefaults, .xrdb, or whatever X resource file is in use.
With respect to the latter, please note that the X resource for Ediff customization is “Ediff”, not “emacs”. See Window and Frame Configuration, See Highlighting Difference Regions, for further details. Please also refer to Emacs manual for the information on how to set Emacs X resources.