Wanting to switch to the newer blade fuses is like opening a can of worms. Basically, on the old style glass fuse type, everything splices together at some point and converges into the fuse box run by the 4 glass fuses.
To get to the new blade fuse type, as annoying and tedious as it is, you'll need to break out the splices and run everything you want on individual circuits. Just follow along on the diagrams you have and watch what splits to where.
I rewired my entire car, but went a step further than just the fuse box. Here's what I did:
My car had absolutely no wiring in it. I had a parts car that I gutted the entire wiring system out of (old glass fuse style). I ran that in my car.
Then, I ordered an entire wiring kit that included the newer style blade fuses, only everything was already run onto individual circuits. I ran everything in the car side by side with the original wiring.
Here was the hard part (and what you're trying to do). I then got the book of electrical diagrams for the car so I could see what did what and what went where and ran where. ONE feature at a time (ie brake lights, reverse lights, etc), I slowly cut out the old wiring and either removed the factory connector if I could or spliced onto it and terminated the new wiring using original connectors.
Again, I did this ONE feature at a time and moved on to the next, until eventually each section of the old wiring was removed, and ultimately until I got to the last set of wires behind the gauge cluster where I finally snipped out the last wire which removed the glass fuse box and made the new system dependent on the new blade fuse box.
I kept this all straight by doing one thing at a time and writing on the diagrams next to the existing wiring "ok this is the original wire #whatever, and it now runs off of the new wire whatever".
If you start cutting multiple wires and trying to do the wiring in sections, you will confuse yourself looking at the old diagrams and trying to figure out "wait a minute, this controlled this this and that, now what controls all that?" That's because the original spliced down to 4 fuses, and now you're breaking that out into separate circuits.
In the end, I ended up with a new wiring system that works off the newer blade style fuses, and everything has it's own circuit. Everything is connected with original connectors and ends. It took me about 40 hours to do the conversions, but initial testing looks like everything works the way it should.
Just take your time and be patient when breaking the circuits out. I had the same initial confusion thinking that one main wire runs the fuse box. It doesn't. If you need to figure out where something gets power, start with the battery diagrams, and follow the wiring schematics to the particular thing that you're trying to get power to. You'll find that most things run into a spliced junction, and everything eventually leads into the fuse box.
The other way to look at it is follow the wires out of the fuse box on the schematics. You'll find out just how many things run off of one fuse and how it got routed there.
Sorry for the book, but hopefully that gave you a little insight into what you're trying to accomplish.
2003 V-6 - the usual bolt-ons. Traded for 2012 V-6
2012 V-6 - premium "Pony Package" edition. Leased, so no mods. Traded up for 2013 5.0
2013 5.0 - premium package, visual mods for now.
1965 coupe - Born - straight six standard issue
Now - 5.0 motor, T5 tranny, R&P, full length subframe connectors, Caltracs draglink bars, hedman headers, disc brakes, MSD 6, paxton supercharger, and probably a bunch of other stuff I forgot to mention. It's loud as hell, and my new toy