>>37
Generally software that allows the user to edit the toolbars and menus also has an option for saving presets and reverting to default layout so that sort of removes this problem.
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I think many of the challenges in interface design stem from working out a good hierarchy for the menus and toolbars, which controls should be grouped together for maximum efficiency, where would a user expect to find submenus related to various functions. The two most obvious solutions would be to either conduct a sort of 'time and motion' study of how the user interacts with the interface or as stated above straight copy the interface conventions of similar popular software.