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Govahnator
I am having the same issue, i just installed my new e3d v6 hot end and i cant get the fan running
You are both having two separate issues. The e3d fan that connects to the hot end itself should be on all the time. There is a dedicated pair of pins just below the first stepper driver above the two big fuse things.
For the fan attached to D9, download Repetier (as I can't remember how to do it in pronterface) and use the slider I've highlighted below when connected to the printer. The fan should come on at anywhere between 0 and 50pc along the slider.
If it doesn't, few things to try,
With a multimeter check you've got voltage coming out of D9
Try reversing the wires on the fan
After that it's going to be a look in Marlin. YOu need to find the section in pins.h related to motherboard 33 and in that section (and only in that section look for the fan_pin setting. Should be 9.
This is what mine says.
#if MOTHERBOARD == 33 || MOTHERBOARD == 35 || MOTHERBOARD == 67 || MOTHERBOARD == 68
#define FAN_PIN 9 // (Sprinter config)