The trick to fiber optics is getting them aligned as nicely as possible above the LED, for maximum brightness.  

This 3d printed cover fits right over the Pixie LED and holds up to 20 fibers in place right above the light.  If you're using 3 fibers per ruffle, that works out to 6-7 ruffles per light.

I found that printing in black filament seemed to work well -- the Pixies are so bright that they blow right through a lighter color of filament and wash out the fiber optic lighting.

If you don't have a 3d printer, you can order them from shapeways. 

Print them with a nice high resolution, with minimal supports.  

Poke a hole at the top of each ruffle and slip all the fiber leads through to the inside of the dress.

You'll be hooking up multiple ruffles to each Pixie LED.  I had 30 ruffles and 5 Pixies: 30/5 = 6. That means 6 ruffles, containing 3 strands each (18 fibers) per Pixie.

I wanted the different colors dispersed semi-randomly throughout the skirt, instead of having solid color block sections, which made the organization of the fibers a little bit complicated.  I wanted to keep all 18 fibers going to each light in the same general area of the skirt (to avoid lots of fiber leads wrapping around my waist) but didn't want them all next-door to each other.

I used colored pins to mark out which fibers should go to which light, and gathered all the fibers together and secured them with a small rubber band.   

Be careful to leave the zipper opening or closure on your dress free!  You don't want to fiber yourself into the dress permanently.  (At least, I assume you don't)

Slide all the fibers through the top of your Pixie cover.  Make sure you have enough play that nothing's pulling too hard on anything else.  Clip all the fibers at once so they're exactly perfectly the same length.

Slip the fibers through the case until they're just at the bottom of the fiber tube.  Place a Pixie LED in there temporarily, and press the fibers down so they're touching the top of the LED.  Make sure all the fibers light up.

On the outside of the case (at the top where the fibers go in), coat the whole assembly liberally with E6000 glue.  Don't use hot glue or crazy glue here -- hot glue could melt the fibers, and crazy glue will make them disintigrate, stop carrying light, and break.  (Ask Me How I Know)

Once you have all your fibers managed and glued, and the glue has dried completely, sew each Pixie LED into its case using the mounting holes on each side.  Watch it GLOW!