I don't know specifically what paints you use, 
but this is what I have found successful,

I use golden brand fluid acrylics. In addition 
to the fluid acrylics, I use an acrylic medium 
called "tar gel". This medium helps the paint 
lay evenly across the acetate. Thus - keeping 
the "light areas" from hapening...
The results actually appear to be more like real 
cel paint (with the exception of the shineyness)

Ok - the catch? It takes a little bit more time 
for the paint to dry with the tar gel medium. 

And one thing I do to prevent any dark colors 
from going over light areas is to just be 
careful painting them. And if it's possible - 
paint the dark areas first. Dark and/or small 
should be done first. 

I hope this helps.

Also, I found a tool to draw the lines on the 
top of the cels - *doesn't know if you know 
already*... but it's called a "ruling pen".. You 
just drop a little paint in, practice a _lot_ 
and then you're on your way ^^

email me if you have any questions...

~Tara