We're having the same problem with our waterer. Last year, I did raise it up with a wooden platform, but this year, the smallest chick (silkie) is a LOT smaller than the biggest chick and the minimum I would need to raise the waterer would be too tall for the silkie.
I saw on here once...I can't remember where though...somebody had built a brood box that was set up in such a way that the waterer and feed trough were not on the shavings. They were on chicken wire, I think, or something like that...so the chicks could eat and spill food to their little hearts content and it would just fall underneath the wire...and no shavings could be kicked in.
I wish I could find that setup again. Because when I design my next brood box, it will totally be set up that way.
I put a flat rock on one side next to my waterers for my Frenchy to climb up on since she's smaller than the others. In the brooder you could do the same thing.