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If you're referring to the way the windows are scattered all over, you have two options. Either

1) Manually place the windows the way you want

or

2) The AU also supllies different preset window placement files that you can select from (according to your resolution). If you decide to go this way, you will need to rename the file to the servername_charactername_eq2_uisettings.ini format, as it will have the appropriate screen resolution in place of the servername_charactername part of the file name.

Use the "Window Wizard" supplied in the ThorUI AU within "options"
(It's the middle of the three square buttons)
I recommend 1280x1024 Full Screen (Just make sure you can play in that mode.)
You will also need to go into options and remove the widescreen/black border option.