It depends on whether you want to add mods in yourself. If you do, Logistics Pipes is definitely the way to go--you can request anything from inventories in its network and you can teach it to craft stuff for you, too. It can be very confusing for the beginner, though...I'd personally recommend direwolf20's Season 4 episodes where he builds his Logistics network and iirc there's an unofficial Logistics wiki floating around somewhere, that's how I learned...
If you DON'T want to add extra mods, you have two options (that are conventional). One, you could use Barrels so you have a wall of pictures of items that you can just click to take from. This could be paired with a router, but I'm not a Factorization whiz yet so I don't really know much about it besides that it seems fairly nifty.
The other conventional option is sorting machines/sortrons from RP2, although the latter tends to not be super user-friendly and you'll need some FORTH chops (or chops in whatever RP2 interpreter you've chosen to load).
Hope I helped. I personally went with the Barrels option, since it's the easiest to set up. I would've switched over to Logistics Pipes but then I went into minecraft-hibernation waiting for the new packs.
