Brush work is absolutely harder to do than using  
markers, but the line tends to be more solid, 
which looks better. Also, I have yet to find a pen 
that makes a good smudgeproof line- Sharpies are 
permanent, but the ink has a funny reddish shine 
to it that doesn't look authentic- it doesn't 
match cel ink.
Once the paint dries, I don't think you'd have any 
problem with the mist layer adhering to the paint- 
 small lines generally don't cause sticking 
problems, it's usually large areas of color that 
stick. Just so you're not exposing the cel to 
temperature extremes now that it's safe in your 
home, I don't think sticking will be a problem. 
Still, if you worry, you can always put a plastic 
sleeve on the mist layer so if there were any 
sticking, it would be to the sleeve, not the mist 
layer.
Blair