Every time I start a project with some graphical toolkit, one of the first conflicts happen with the decision of how to deal with the visual design and the widget layout: A grap
It depends on the number of different windows/panels you need for your application. If the number is small, use a graphical tool. It is much faster to get a few windows designed perfectly. If the number is large, the graphical tool can (and should) only be used for prototypes. You need to code the layout to be able to make application-wide changes at acceptable cost.
That includes creating a model of how the UI of the application works and dynamically adding and removing widgets at runtime. For an excellent example of such a model (in a different environment), take a look at the glamour model for creating object browsers.
I object to the suggestion that it is tricky/subjective (at least more than other development choices). It is easy to come up with criteria to decide on. Personal experience and preference are important for that, as they decide when the number of different windows should be considered small. The same goes for tool quality.