All these aftermarket fan controller's suck. The thermal switches fail or the relays themselves. Maybe it is the amperage draw of my Stratus fans but the last Flexalite fan controller didn't work at all.
Starting a high amp fan on 12 volts will really load a system. The amp draw is super high until the fans get to their natural speed. Even with a controller (unless it was a PWM controller), I would have the controller turn on cheaper, replaceable relays.
I try to run dual fans in series then switch to parallel when the motor gets really hot. Dual fans in series draws very low amps, and since they are already running at 1/2 speed, the amp spike is less when they switch to full speed.
The only drawback with this (other than needing an extra relay), is if one fan dies, both fans die... until it gets hot enough to switch to parallel, then the good fan will kick on.