Tks but what do you mean by covers?
It's a redpower thing. You can hide redpower pipes and wires with covers.
The truth is that there are many ways to do what you want to do. Direwolf20's favorite approach is to use redpower2 sorting machines, but you can do it with buildcraft pipes or Factorization routers or even (with a bit of cleverness) railcraft stuff or Steve's Carts.
It would help us help you if we new what kind of resources you have available. Redpower's stuff is the cheapest, but also invovles specialized tools. Factorization's stuff is really really powerful, but you need a diamond block, obsidian and TNT to start. Buildcraft's stuff is not very smart and costs diamonds, but can do a serviceable job. Do you like Thaumcraft? You can make a sorting system with Golems and it's actually very space efficient!