Some ECU's have this capability - some do not (running two fans). If not - you can control two fans with the SPAL PWM controller or similar. I like the SPAL version - it is easy to use - water proof - and with the addition of one relay will run twin fans. I like it's strategy of running the fans for awhile after turning off the A/C for a cool down period etc.
I know the FAST EFI has dual fan control... as did my Accel Gen 7 ECU
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