Hi Art, thanks for those kind words, I'll do my best to explain.
I run wires from both the left and right side of the cargo area of the Jeep from where the roll bar attaches down to the cargo tub. On the left side it's mostly stuff related to the Manager 30 and on the right side it's for the inverter and also a power feed to the SPod. Unfortunately I don't have any pictures with the trim, fenders, or carpet out of the way.
There's a spot at the top of each wheel well where you can drill a hole (I used a step bit) where you only go through 1 layer of sheet metal and don't have to interfere with any weld points or anything (it's actually a slightly different spot on each side). I then painted the raw metal and used a rubber grommet and some butyl rubber tape to seal it up.
Here's a shot of the right side with the carpet pulled back where you can see the grommet:
There's a decent amount of space behind the carpet and under the plastic trim, I was pleased with how nicely things went back into place. You can see in the above picture I relieved the plastic trim piece to clear the large inverter wires but that was not needed on the left side where I running more reasonably sized conductors.
To run from the top of the wheel well you go behind the inner fender liner. The best way to do that is to remove the rear fender and liner in one piece. Look for 'removing JL fenders the easy way'. I've removed my fenders several times over the last year and a half and it seems the plastic clips are getting brittle enough that I break some when I do it now. When it was brand new I don't think I broke any. Anyway, here's the Mopar part number:
68526185AA
The wire bundle goes along the inner fender (there's some factory wires running the same path) and then turns underneath near the rear shock mount. Sorry I don't have a good pic but there's one obvious place that keeps the wire out of the way of any suspension bits and up as high as possible.
Here's a couple of bad attempts to show the wiring by the cargo tub:
Here's where it's going up into the fender well (left side):
And here's where I use cable glands to enter the cargo tub:
Please excuse the frayed wire loom
As you can see cable protection is important, I'm using both a flexible loom and also the hard split conduit, especially important where it goes around the frame and up into the wheel well.
Here's where the wires above make their way into the cargo tub:
Running wires this way on the passenger side has a difficulty factor, this is where the evap stuff is on the JL, this thing is sitting at the top rear of the passenger wheel well:
I was able to remove the bolts holding it in place and lower it enough to run the cables on top of it.
Happy to follow up with more details, just let me know, and I'll reply to the Arduino question a bit later.