to be honest, it is REAL easy...just take your time, follow the instructions, solder all your connections if possible, and you should be ok.
As for onboard chargers, I have had Guest and ProMariner models and they have failed for me. I have a small dual pro charging my cranking battery and that hasn't yet failed
As for how close your batteries are, it is better to have shorter battery cables, but I wouldn't be too concerned...Most bass boats have all their batteries way in the back, and run the wires all the way to the front.