You could start with a separate fuse box for the parts you want to remain "live". Then connect the hot leads from that fuse box to the stereo and whatever lighting or accessories you want to be able to use. You can then install your "kill switch" to the positive feed (battery +) to the existing fuse box. You can buy small circuit fuse boxes for not much money, or just go to the junkyard and get something from a donor vehicle.
If you have circuits that are live when you open the kill switch you've installed, then you have wiring problems that need to be addressed before you proceed with any new wiring to achieve your goals. You can, however, get a battery disconnect that attaches right at the battery + lead, that you would have to lift the hood to turn on / off, but work very well. They too are not expensive.
Automotive wiring is not trivial and if not done correctly will give you more headaches than you can possibly imagine. If this install is over your head get someone who knows what they are doing to do it instead. Emphasis on "knows what they are doing", not someone who just says they know, because there are a hundred wrong ways to do this. Just by way of example, you have to buy the correct wire, and "Primary Wire" sold at your local auto shop is not for interior or underhood use; it's for hooking up trailer lighting only. Just an example.
Maybe your buddy should be calling Painless Wiring (Google them) and explain what you want and what they recommend. They are not cheap, because they use the correct materials and correct wire, and although everybody wants The Donald to Make America Great Again, nobody wants to pay for Americans to make wiring harnesses when someone in Shenzhen can do it for $100 cheaper. But if you do, they are the guys to call.
