Newbie here! Is there a way to control a 12V fan that is connected to a relay with PWM?
Any links would be helpful.
Thanks
No. A relay can't do PWM.
If you replaced the relay with a MOSFET motor driver, then it could work.
Here's a better trick, eliminate everything between the motor and Vcc.
Transistor is something like an irlb8721pbf, N channel, logic level MOSFET.
Hi,
What is the fan, if its a BLDC fan it may have probems with PWM control.
Tom.. 
A standard computer fan has its own motor controller built in and can only sensibly be speed controlled
by the speed control input (if it has one), or by setting the analog supply voltage (within limits).
Trying to PWM the entire motor controller will be pushing lots of big current pulses into its decoupling
capacitors - the behaviour will depend on the design of the fan control board.
You can use slow PWM perhaps, 1 Hz or so, to power the fan up and down on a shorter timescale than
it takes to spool down.
So how do I wire this with two 12v dc Fans that Have a 3pin connection in series or parallel?
A 3-pin fan is most probably one that has a tachometer output. It has no speed control. A 4-pin fan would be better because it can be controlled directly from the Arduino pin.
You can only control the speed of a 3-pin brushless fan by controlling the power supply voltage. You can do this by making a PWM-based power supply but that's going to be relatively large, bulky, inefficient and expensive.
Buy fans that are intended for this speed control.