I just found out how to resize the gnome-do docky:

  1. right click on the gnome-do icon in docky and activate either the trash or the clock
    that's the only way i found to get a divider into docky
  2. hover over the upper border of docky (directly above the divider) and you'll get the up/down arrow shown
  3. click and drag up/down to resize docky
that's it ... long search but trivial solution ;)