You want to penetrate the penthouse top on the outside of the PH fabric. This will prevent any water leakage getting into the interior. On ours I then loosened some of the screws that hold the fabric to the top to allow the wires to pass through near the drivers side corner of the penthouse. Then retightened the screws. Once the worse were inside I routed them down the PH fabric next to the wires that fed the PH lights. Unfortunately I did not take photos.
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Current van: 2002 Ford E350 extended body camper with Colorado Camper Van pop top and Agile Offroad 4WD conversion.