The red wire from the rectifier is power out of the rec to charge the battery. The only time power flows through that wire is when the bike is running, it don't need a switch.
Do you know what a diode is? If not, it is a one way valve for electricity. The rectifier is three pairs of diodes that are linked together to convert AC voltage to DC voltage. They are set up so power only flows from the rectifier to the battery.
The only way for power to flow from the battery to the rec on the red wire is if at least one of the six diodes are bad. Seldom happens.
On the 20 amp fuseyou want this between the battery and the rest of the electrics. This will protect, in case of a short in the wires from the fuse, through the main switch to your fuse box. You could run without but carry a fire extinguisher, it may come in handy to put oiut the fire.
An inline fuse holder works well. I like to wire the rectifier red wire right to battery positive. I then hook the fuse to battery positive. You can hook the rec red wire after the fuse, either way is fine.
On the 20 amp fuse holder I hook one lead right to the battery. Then run wire from the other lead to the key switch. You want the main fuse as close to the battery positive as you can. That way it can protect as much of the harness as possible.
On the brown wire after the switch it is hooed to both the reg/rec as well as the brushes. For the alternator to make electricity it needs a magnetic feild created in the rotor. It creates this magnetic feild by running battery voltage to the brushes on the brown wire. This voltage flows through the bryshes and rotor and out to the reg on the green wire.
Now the reg reads battery voltage on the brown wire. If the battery voltage is below the preset 14.5 volts the reg turns on the transister and this grounds the green wire. When the green wire is grounded the power flows, creating the magnetic feild, exciting the stator into producing AC voltage. This AC is sent on the three white wires to the rectifier where the diode sets convert it to DC then is sent to the battery on the red wire.
This charges the battery. As the battery voltage rises and reaches the preset 14.5 volts it turns off the transiter, stopping the power flow and the alternator stops making electricity. The voltage drops below the 14.5 volts it turns the transiaster on, restarting the cycle. It repeats the on/off cylce thousands of time a minute so the battery stays at 14.5 volts.
On the older seperate reg/rec the reg did it's thing before the rotor instead of after and being mechanical was much slower, it only cycled hundreds of times a minute.
Leo