I think I may have a similar problem installing EQ2MAP_Updater_0.97_Setup.exe.
On install had 'request confirm EQ2 directory box', which listed the correct location for EQ2 game files (C:\Program Files\Sony\EverQuest II), so I accepted it.
Now eq2ui_mainhud_map.xml, eq2map folder, and images folder, have been created in C:\
There is no sub folder in UI (except Default and fonts).
It doesn't look like eq2.ini has been updated either as it only contains: r_aa_blit 1
A
really clear list of which files/folders your installing and where they
should be would be real handy. Also exactly what the replacement eq2.ini should finally contain would be good. At the moment I don't know what files should be where, or if I'm missing any.
I know it's a pain, but this stuff should be included with a general release beta.
On the bright side this is no way as big a hastle as installing the 50+ mods i run under Morrowind!