The A spot is where you want to add your wires on to. The B spot that you labeled looks like the alternator socket. That has nothing to do with the big3 so dont worry about that.
As far as where the stock wiring runs, fuck it. Its just Honda's was of cleaning up the engine bay, they just weave it around the engine in order to make it looks a little neater and such. Just do the straited and more direct path that is or course out of harms way as well.
You need to upgrade the alternator + to the battery +
Battery - to the frame
Battery - to the engine block
And if you want you can do the fuse blocks which are battery + to fuse left and alternator to fuse right (double check your layout to make sure left and right fuse block spots)
And when you put the ring terminals on, take off about 1/2" of the cable sleeve to expose the bare wire. Take the ring terminal and dont twist it up, just pinch it together at the tip and slide it in the bottom end of the terminal. Take a hammer and hit the middle of the ring terminal on the front where the two ends meet. This will push them into the wire. Then turn the terminal on its side and hit it from the side so that one of the sides will go underneath the other making a nice tight hug around the wire. I really advise this part so that the terminals do not slip out.... Heat up the end of the ring terminal with a blow torch (a hand held one from HD or Lowes will work, its what i used) and then heat up that fucker for about a minute making sure its hot as hell. Then quickly, take about a 2 ft piece of solder and push it into the front of the terminal where the wire is. This will melt the solder and let it drip down into the wire forming a nice bond between the wire and terminal so that it will NOT fall out when driving. Check out Meade's thread about how to do it with pictures.
Good luck man, its really easier than you think its going to be.