Plus a cover just makes the look a little cleaner.

I did mine similar to yours but pushed both batteries further in. That way I could run the wires straight down from the switch and back to the batteries. Mine don't run through the hole in the floor like yours but I think you could do the same and tuck them under the lip of the passenger helm support to keep them at bay. I think Al Cab acutally drilled holes through his support to feed the wires so he didn't have to run them underneath and be exposed.

Top cable goes to breaker and then to amp distro.
Two smaller red cable coming in are from the batteries.
Larger pink looking cable goes back to the starter.

I don't know if your batteries would crowd that front amp though. May get ugly - but hey, just move it! You didn't really think you were done yet did you? Now that you've thrown up what you've got all the other ideas will start popping up.

Time for a new amp rack...