The "Solar Prep" package on the Holiday Rambler that I installed a 400 watt solar system on was "Drill a hole in the roof here, and pull out the wires". So I measured 15" from the sidewall, and 10" back from the skylight, and cut a hole about 1" diameter, fished around with a coat hanger for 10 minutes and pulled out about 4' of #6 wires.
Sealed the hole with a lot of rubber roof sealant, and have a water tight handy box on top of the hole, with the solar panel mounted above that, so the box will never see any rain.
My suggestion? Cut a hole in the roof that will end up under the solar panel, and put a box over the new hole. Make sure that the hole will be over a cabinet that you can run the wires through without them being visible. You might have a TV cabinet you can run the wires through, or a closet that the wires can be routed in a way they can not be seen while looking into the closet, without climbing inside.
I ran #10 UV cable direct burial wire between my panels, and also to the controller. I have one pair of 120 watt on one #10 wire and 16 watts on the other #10 wire. This goes to a 50 amp solar boost controller, and #8 wire running to the batteries.
Thats how I ran mine and it worked out fine. I was able to run them from the top of the vent and came out under the bathroom sink where I could easily fish them through to the basement. I also caulked up the pipe and no problems.
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