You can still have them come on with the ignition switch using a relay (wiring 101), The idea is to pull your power from the source not the alternator, using a relay is eliminating running high voltage past the firewall and having the shortest power source to the fans, Maybe a read on basic automotive wiring is in order.
Rattrap,
The amperage doesn't pass through my firewall, I have eliminated all of that wiring, the fans come on with a 12v keyed relay and the power for all the extra components in my car are fed from two new fuse blocks that are independent of the factory fuse block.
