My fan controller runs off of a constant +12V power source (the battery). This is so that the fans can continue to run after the key is switched off. I feel that I have a very simple setup and it has been working well for several years now. If you really must have a switched power source, you could tap into one of the circuits that make up the underhood fuse box, just make sure that you tap the fused side, or better yet, tap the other leg and add your own fuse/circuit breaker and relay. If your fan controller doesn't incorporate a relay as part of it's design, I would consider it a necessity to add one. My (adjustable) fan controller is an off-the-shelf item from AutoZone, and it came with a 30 amp relay.
