Dont get me wrong JK, nothing wrong with your setup at all. Gives you one hell of a ballsy battery setup and will prob serve you perfectly well, it just wasnt what you described thats all. And as for your black spagetti, well, it just took me by surprise I guess
To be honest with all the black cable covering its a very professional job, just havent seen a battery with that many things connected before. I also think that the black covering being a lot thicker makes it look like a lot more stuff.
There are a few options to what you want to do, so as isolators and fuse boxes etc.
Personally, if I go down the dual battery track (one day...) my plan is what you described. Keep the original battery with the original stuff connected and a second battery with all accessories on it. Then set up an automatic battery isolator that will keep both charged, keep accessories running only off the second batt, and kick in the second to help the main if its running low during starting for any reason (same as the setup we put together for the old mans caravan).
The second fuse box idea is a good one, that would enable you to tidy it up and easily identify different circuits if required. Its a brilliant idea to put in first, but prob a lot more of a pain to put in later (like now as in!)