Since I don't have my iLiad, I don't know how to show hidden directories in emelfm2.
Likely, the easiest way is to copy the file with mrxvt (or create a .sh file with unix formatting) to your cf card or internal memory.
mv /mnt/setttings/.FBReader/ui.xml /mnt/cf/
Make the changes you need on a PC. Save in the same place. Then:
mv /mnt/cf/ui.xml /mnt/setttings/.FBReader/