Well, from a chest you should be able to put more than one filter on said chest to pull more than one stack per redstone cycle. Or more retrievers if you are building a system like that.
It becomes a whole lot easier if you install the Logistics Pipes mod, as it allows you to pull one stack a tick with the highest revision module for such things. My quarry system gets backlogged around 25mj/t on a single quarry with just filters and retrievers. With log pipes, I don't have any such issue. They are a good deal more expensive, though, so start with redpower2 (or buildcraft if you are feeling adventurous) to make a simple sorting system, then redesign it when they add log pipes/add it yourself/add a lot more filters/retrievers.
Good luck!