So, after much fighting, I've got my z - probe moving, the problem is that when it give the command for up (M401) the probe goes down and vice versa. Similar story happens when I enter G28 and G29, when it goes to probe the z axis it lifts the probe instead of lowering it.

Is there a place in the firmware to invert the direction? If not, what other options do I have?

If the movement is opposite of what you tell it to (x1 and it moves in x-1) then just flip the motor connection. When homing the firmware tells the printer to raise up a little before coming down to probe

That won't cause it to hit the hot end, will it?

Oh, never mind. You are talking about the servo arm. Did you buy a reverse servo? There is no way of reversing the servo that I know of, other than doing some re-wiring inside the servo or flip the arm to the other side.

Nope, its a normal servo

[www.pololu.com] Thats the exact one that I have

What values are you using for your servo locations? I think I have found that parameter in the firmware, maybe if I put in different values that would fix the problem?

You need to set the angle for the servo arm for the probe. You'll use M280 P0 Sx (where x is the angle for the arm.) to figure out the numbers for extension and retraction angles.

For example with my servo M280 P0 S10 moved the arm to the correct position for retraction, and M280 P0 S88 was correct for extension.

Then you need to edit this line in the Marlin Configuration.h file.

//smartrap : version pololu servo (dark blue)

#define SERVO_ENDSTOP_ANGLES {0,0, 0,0, 88,10) // X,Y,Z Axis Extend and Retract angles

Hope that helps