Well, you can do one layer thick, but I try to do 
thick layers, as in paint it, let it dry, hold it 
up to the light, check it, if its not ok, put 
another layer on, let it dry... 

Some types of paint are a lot thicker and opaque 
when they're wet as opposed to when they're dry.  
If you're holding it up when its dry and you 
still can't see through and you get marks... I 
don't know what to tell you.  

I think I'm getting a light box for Christmas, 
which I hope will let me do all sorts of new 
tricks I've been dying to try.  I'll let you know 
if if helps with the paint transparency problem.

don't get too stressed, animators have it a lot 
easier than amateurs do.  Have you ever looked 
really closely at the lines of a cel?  I don't 
mean the black ones, I mean the edges of the 
colors. Lots of times you can see that they 
outlined the color section before they painted it 
in--same color obviously, so its hard to pick up, 
but the texture is slightly different.  Handy 
huh? A friend who's into crafts told me she knows 
someone that has custom-fillable paint pens, 
which I think must be what animators use.  Oh 
man... what I wouldn't do to get my hands on some 
of those.