The nozzle size does not affect any of the maths in skeinforge because it doesn't influence the volume of plastic that flows through it. It just affects the maximum layer height you can use and the minimum filament width.
As long as you keep within the following limits it will work.
Filament width >= nozzle diameter.
Filament width * layer height < cross sectional area of filament extruded into free space.
Filament width > layer height * 1.5
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