I'll give Tuxedo's transistor setup a try... Should work. The PWM freq. from the Pololu motor controller was too high, that's why the fans didn't respond. PWM would actually be the preferred method so I can set different fan speeds for different temperatures.
** What radioshack friendly transistors could I use to setup a pwm circuit like the one Tuxedo mentions
Pin 6 goes to a 1k resistor which goes into a bc237b base. bc237b collector to +5 and emitter to a 1k resistor, to bd135 base. Fan red wire to +12v, black to bd135 collector. bd135 emitter to gnd.
?
Again, sorry for lacking so much electronics knowledge lol I knew more a few months ago when I was learning something new every day, but then I stopped working on Arduino projects for a few months and now I'm back to stupid.