Controlling two 4 wire fans using Arduino
I honestly can't tell what is written on your drawing or what is connected to what, so here follows a general answer:
The Arduino output is 5V (or 3.3V) so you can't control 12V fans via the power pin without transistors (even if you get 5V fans you will have current limitations). Some of these 4 pin fans will not even turn on reliably depending on the duty cycle (or will shut down randomly) if you try to PWM via the power pin.
If you have 4 pin fans I highly recommend controlling them via the PWM pin since they accept 5V signals (so you can control them directly with the Arduino PWM pin):
From &quot;4-Wire Pulse Width Modulation
(PWM) Controlled Fans - September 2005 1.3&quot;:

From Noctua PWM specifications
white paper


In this case, the flyback diode is not necessary as the speed control is done inside the fan. The necessity of a bulk capacitor will depend on how you system is wired. In general, they are not necessary but 10uF across the power pins of each fan won't hurt either.
Note that the spec says 21kHz to 28kHz, AFAIK the &quot;standard&quot; Arduino PWM frequency is around 440Hz (or 1.1kHz), so you might have to modify the output frequency. (You can try the standard frequency, it might work).