The .ini file is typically stored in directory (folder):
\Documents and Settings\USERNAME\Application Data\EQMOD
USERNAME is your windows login username). The Application Data folder has hidden attributes . This means you might not be able to see the folder. Set your explorer options to show hidden files.
You can also just enter
%appdata%\eqmod
in a windows explorer address bar, or
%appdata%\eqmod_sim
for the simulator ini's.
There are several .ini files.
ALIGN.in
EQMOD.ini
EQMOSAIC.ini
EQTOUR.ini
JOYSTICK.ini