Smoku already said that resizing the screens by fractions is not going to happened, so its either original or double the size. That limits the amount of layouts one can have.

EDIT:
If you want some numbers on the screens

the N900 = 480 height and 800 width (in portrait mode these are swapped)
the N DS = 192 height and 256 width (both the screens are)

so the width on the NDS screen times two is more than the height of the N900, this means that even in full screen you would have a crop when playing it in double size at portrait.

Side by side the nicest IMO would be to have one double and one normal size.