Just in case anyone has not yet come across this: http://darnified.net/forums/articles/configuring_ui_33.0.html this site has proved for me at least to be Very Useful Indeed.

I realise that this is probably old news but I thought I would post it here just in case anyone else was wondering how to make their settings stick.

Thanks for the link. That's a resource I had missed.

-Dubious-

Also note that kyoma made http://oblivion.nexusmods.com/mods/34792 which makes the changes you make in Darn's configuration menu while in the game to stick between game sessions.
However, editing by hand is still preferable, since there is a delay before the mod adjust the menu values to what it remembers from the last session, and therefore mods that rely on those values like theNiceOne's Hud Status Bars can get erroneous data and your bars might end up messed up.