I have 2 fans and they require up to 3A current, but my motor shield (Arduino Motor Shield Rev3) on my Arduino MEGA can only provide 2A per channel (4A max). Is it ok to run the fans at a lower speed or are there other options to run (H-bridge)? Thanks.
I kinda doubt that that fan will actually draw 3A. You could probably get away with using your shield--just measure the fan current draw by directly connecting it up to a 12V supply and measuring with a multimeter.
If it actually draws 3A, any of these sounds like a decent idea: