Once PCB view is in a good spot you can check the schematic svg. It is in FritzingTest\parts\svg\contrib\schematic
You'll notice that the svg converter is smart enough to make pins for all the through hole pads but did not create pins for the SMT motor pins
You can add 'missing' connectors easily. Go to params file again to find the two pads that are used for the motor:
Cut these lines and place them in the group above, in the <left> xml group, that will put the pins on the left side.
Now is also a good time to rearrange the pin orders if you want them to appear in the schematic in a certain location or order
Rerun the tool to regen the schematic
You can hand edit the schematic and move around pins, but you'll need to reassign the pins later, just keep eveything on a 0.1" boundary to keep with convention. Since Fritzing isn't known as a hardcore schematic capture program we don't spend a ton of time on it.
You can edit the name/labels of the pins easily. Just make a backup because you'll rerun the tool to get breadboard view right, which will overwrite your changes! We find it a lot easier to update the signal names directly in EagleCAD, that way you aren't editing signal names in multiple SVGs