Since every single time I start Mathematica, my first action is aligning the windows properly (Notebook on the left for $2/3$ of the screen, help on the right for the other $1/3$), I was wondering whether this could be done automatically. This is what it looks like:

How could I make Mathematica to use these window positions and sizes by default?
SetOptions) theWindowSizeoption on allNotebooks[]but the documentation one for window size,WindowMarginsfor window positions. Get the usable screen size (sans Gnome panel) withScreenRectangle /. Options[$FrontEnd, ScreenRectangle]. Sorry, no time for a proper answer, but you should be able to work out the details going from here. – Szabolcs Feb 11 '12 at 23:29System/Guides/Mathematica.nbso it seems the position of that is controlled elsewhere. – Mr.Wizard♦ Feb 11 '12 at 23:53