Hi Pirates, based on Hein's comments, I'm going to try to explain how is the mixing of the motors done, depending on the layout/position of your ship's motors.
All mixing depends directly on the motor's positions and layout proportions. Depending on it's position each motor needs to apply different strength to pitch and roll axles. In other words, the farthest a motor is from a axle, the stronger it will have to pull.
This strength is set for each motor in the motor mixing (motors.pde) as meanings of a percentual value, that will multiply pitch and roll values used to calculate the final value for each motor.
When the percentage is 100%, it is not necessary to add any value, as we would be multiplying by 1.
Pitch and Roll Axles
Pitch and Roll axles will be used as reference to find the needed strength for each motor:

The axles layout will help to understand and locate what will the values for each motor be, and it's sign.
As for the Yaw, things are simpler, as it just depends on the rotation direction of the motor:
If Motor turns ClockWise (CW) Yaw is Negative.
If Motor turns CounterClockWise (CCW) Yaw is Positive.
I will try to explain it using exampes for the frames we commonly use:
Quad + mode
Ok, let's start with a simple Quad in + mode:

As all 4 motors are on the axles, they all will have 100% and 0% as strength values, in more detail:
Motor | Pitch | Roll | Yaw |
0 Right CCW | -0% | -100% | + |
1 Left CCW | +0% | +100% | + |
2 Front CW | +100% | 0% | - |
3 Back CW | -100% | 0% | - |
Thus the resulting pseudo-code would have these signs and values:
rightCCW = - (0 * Pitch) - (1 * Roll) + Yaw
leftCCW = + (0 * Pitch) + (1 * Roll) + Yaw
frontCW = + (1 * Pitch) + (0 * Roll) - Yaw
backCW = - (1 * Pitch) - (0 * Roll) - Yaw
and the final code in Motors.pde, adding throttle and controlling total motor value not to get out of bounds, would be:
rightCCW = constrain(throttle - control_roll + control_yaw, minThrottle, 2000);
leftCCW = constrain(throttle + control_roll + control_yaw, minThrottle, 2000);
frontCW = constrain(throttle + control_pitch - control_yaw, minThrottle, 2000);
backCW = constrain(throttle - control_pitch - control_yaw, minThrottle, 2000);