Yeah that part was kind of strange to me too. I plugged my passenger side one in cause it was closer to battery and then ran the longer wire over to the driver side, but I imagine either way would be fine.
Link isn't working but I purchased this kit online:
True Mods H6054 H4 LED Headlight Wiring Harness [Negative Switched Conversion] [Fused] Universal H4 Head Light Relay Harness Kit for 9003 H5054 H6054LL 6014 H6024 6052 6053 Subaru Toyota Jeep...