This is a system which works for me :)
At Display Products I've found these amazing plastic boxes, all comes with a lid, so all dust can be kept out and also wont the paper be messed up.
The tiniest box is called a playing card box and it warks perfectly for brads, pearls etc. and the lid comes of so easily.
These boxes are called calling card boxes, they are great to store brads, embellishments and other small bits where the amount is too big to be in the smallest box. These I have 100 of till now.
And this is the smallest box, the playing card box, of these I have bought around 250 of till now.