The wires between the pellet box and smoker, are for the temp probe, which really can't be moved, and for the hot rod, which run down "through" the pellet delivery box (under and outside the auger), and when I replaced my hot rod, I certainly didn't see any better way to run them. I ran them back through the way I pulled them out. I have no trouble what so ever with the wires interfering with the fan, or the air flow. You may want to look under the pellet box, and make sure the wire bundle is wire tied our of the way of the auger motor and the fan, but mine was fine from when I first put it together.