Let me see if I can help.
I would say for about 99% of you out there, the fans should be wired on "high speed" from the factory. Unless someone has done something with the sub-fan short connector, the fans should be wired for "high speed" operation.
Here is the factory wiring diagram for just the radiator fan setup.
http://main.experiencetherave.com/subar ... iagram.pdf
As you can see the sub-fan short connector ties into the same power supply lead.
If you look at the AC wiring diagram it is MUCH more confusing
http://main.experiencetherave.com/subar ... ngdiag.jpg
The jist of that drawing is this. The main fan is on "high speed", and the sub-fan is on "slow speed" unless the sub-fan water temp relay activates to "high speed".
Now....for your custom setup, I would really just keep the stock wiring how it's setup (with the sub-fan short connector connected), and use the existing pin at the ECU to activate the radiator fans through the existing wiring/relay setup.
If that's still not clear, let me know.
edit: Just one thing to add.....the ECU does not control in any way fan speed. The ECU just controls on or off.