The way I run them is the furthest back is the line closest to the tow board, then next one out comes closer to the boat and is in second position from the tow board, the next would be even closer to the boat and the third line down the tow line and so on.
If you are running a horizontal rod holder system (3 rod holders), I would run the one on the left is the farthest out, the middle holder would be the second farthest out and the right holder would be the closet to the boat and last on the tow line.
Otherwise, you will have many tangles.
Ray