I tried to do it with a permanent Rapidiograph 
pen, but those are VERY expensive pens, and a 
pain to maintain as well.  Plus, when I tried it, 
the ink didnt dry right away, and smeared as 
well.  I dont know, Im a casualty of the 
Digitalism age...meaning if there's an easier, 
better way, Im all over it.  Hand painted lines 
are nice, if you REALLY know what you're doing, 
and you have the right tools, and are very 
patient.  I have all of those things....but not 
for cels.  My hand is not good at inking on that 
slick acetate.  On paper, I can do some really 
fine lines, but it's a whole different story on 
that clear stuff.  Plus, some, if not most, 
acetate, will have sort of a film on it, to make 
ink stick better. That makes it hard too, the 
film adds a sticky quality to it, making your 
pens not want to go straight.  Also,you need to 
be careful, if you do use a Rapidiograph, that 
you dont get fragments of acetate inside the tip, 
that is a bad thing for the pen!  

Good luck if you still plan to hand do the lines, 
it is a nice touch, but it's hard!