You'll have to put a thermo sensor somewhere in the system, or swap out the wire harness and ecu. A manual switch will make the bike ridable as an easy fix, but can cause problems if you forget to turn them on. I have one too, and it is very nice to have, but the system still works as normal and will come on by itself.
Reversing the direction of the stock fans makes them about worthless as the blades are designed to work in one direction. Buy some spal pusher fans and it will cool much better.