The green wire is the bit that tells the aerial to go up and down.
The bit that is indicated as "To Radio Switch Terminal" is actually the signal from the aerial and if you look at the aerial itself you should see a (poss black) coaxial cable coming from the top bit of the aerial with a round plug attached.
The green, red and black wires coming from the motor are the ones that power it.
The diagram goes: black wire to ground, red wire to battery +, and then green wire to head unit (so that the aerial goes up when the HU is turned on).
If you want to run it with a separate switch, there are a couple of potential issues. If all that the HU supplies on to the green wire is a 12v constant supply when turned on, then it's easy enough:
black wire to ground, red wire to battery +, and then green wire to switch then from switch to battery + (so that the aerial goes up when the switch is turned on, and goes down when switch is off).
If however the HU sends different signals to the aerial on the green wire (eg a logic/on-off pulse or a negative voltage), then you'd have to work out some circuitry to operate the aerial.
Personally, I would just use the head unit to operate the aerial, and not use a separate switch.
My cheap Sony HU operates my motorised aerial and it's smart enough to leave the aerial down when you're playing a CD and of course it retracts the aerial when you turn off the HU or the car's engine.
