I have a Taig CNC mill with a geicko controller running mach 3.

The x and y move in the correct direction, but the z moves down when it should moves up, and up when it should move down. I've been playing with it for about 2 hours, and have had no luck, searching yielded no results, so please help me, I have cool stuff to be made.

Either change the active state of the Z Dir pin in Ports and Pins, Motor Setup or go to Homing and Limits and choose Reverse option. Both are from Config menu. You can choose either option when using the parallel port but if using an external controller it may be locked to one or the other, for example with the CSMIO controller the Dir pin state has no effect.
Hood