The positive cable does not need protection, but a disconnect switch is a good idea, even if your are not drag racing. It should be run directly to starter positive post. Make sure cable run is protected from heat sources, sharp edges, etc.

Power distribution for fuse panel can be from disconnect switch. This wire should be atleast 8 AWG with a fusible link. The fusible link is always 2 sizes smaller (12AWG) and should be 5-3/4" long.

Run a second wire from disconnect switch (same size) to a remote terminal block in engine compartment. The ouput of alternator will also go to this terminal block. Use at least an 8 AWG wire for this with a fusible link. This second run is your major load side, headlights, electric fan, pump, etc. All loads should have relays to handle that function. The fuse panel side is only for control function. Use a 3 wire alternator (one wire alternators were designed by GM for tractors only, as they run at one constant speed. They also require atleast 1600-1800 RPM initially to cause the field to self-excite. But when your RPM drops back to idle, the field can fall off and alternator output stops. The 2 small wires on side plug are as follows; one is for system voltage sensing and the other provides field from ignition. This wire you install a diode to prevent backfeeding when you turn off ignition. For MSD ignitions this is a must.

Hope this helps.