The best way to correct your first problem is to delete the uisettings.ini files from the characters that are affected.
The second problem is indeed that you edited the wrong file. Everything in the Default folder gets overwritten by the patcher. You need to make a new folder, e.g. \UI\CustomUI, and place the edited file there. I believe you also need to copy eq2ui.xml from \Default into that folder.
Then create or edit eq2.ini in your \Everquest II folder so that it contains these two lines:
cl_ui_skinname CustomUI
cl_ui_subdir UI/