Hello,
Can you modify one part of a figure – the outline of a face, for instance – by morphing, while you modify the rest of the figure by hand-drawing in other layers?
Yes each layer is independent.
You can even turn your morph layer into drawing and edit it if you want to tweak it a little more 
You can also have some frames morphed and others normal on the same layer.
Thank you, great!
One related question:
Can you hand-draw changes in, say, the head in this walk cycle (link below) without messing up the automated cut-up animation?
http://www.youtube.com/watch?v=jleUaNwfrCI
yes it is common to mix cut out and hand drawn to maximise the time advantage while not looking robotic. Heads are often the part which get the extra attention since they are where our eyes mostly watch.
Thank you very much again, that’s fantastic.