I have stored my cels  and binders in archival 
quality museum boxes.  These are acid free, heavy 
pressboard, metal corner reinforced boxes that 
come in a variety of sizes.  The sizes I have 
seen are 8x10x4, 12x20x4, and a much larger box.  
I was able to find them at larger art stores.  
Here in San Francisco, there is a store call Flax 
that has a wide variety of portfolios.

As for line fading, I noticed that reds, browns, 
and yellows seem to have inherent fading as the 
lines in other colors in the same cel do not have 
the same degree of fade.  I also take care to 
store them out of the sun in a cool relatively 
dry and dark location.

Hope that helps.