I followed Stacy Julian's idea and have my embellies stored by color in drawers. I don't have as much as her, so my blues and greens are in one drawer, then pinks and reds in another and so on. My drawers are too small to hold the ribbon too, so those are in a separate drawer of just ribbon stacked spool to spool.
I really like having all the colors in one drawer and it works for me.
Have fun arranging and organizing!