As lilricky said, 2 lines will use all 4 wires in a jack and each pair is the red/green and the yellow/black. Just remember that the pairs need to be swapped correctly. Each pair has a "ring" wire and a "tip" wire. The red and yellow corresponds to the ring wire and the green and black correspond to the tip wire.
In a 4-wire jack the center 2 wires are one line and the outside wires are the other. Since many single line phones come with cords that only have 2 wires(red and green) actually installed in the cord(look at the plug to see this), just plug a phone with a single line cord into each jack in the house and dial a number to see which line is using the center pair.
You could also plug a phone into the jacks on your side of the box outdoors and dial to see which pair is used(which is the first test phone repairman use to determine if a phone problem is on the phone company side or in the house so they know who pays, etc.) except remember that they should lead from the outside box to a junction box inside the house where all jacks in the various rooms are then wired into. Someone could also have alternated wires there to change on a jack which pair is line 1 or line 2.
So also check your junction box in the basement or whereever it is. Keep the same color coordination for each line.