We did a similar controller this year as well. Although, we only controlled one axis. We made a scale model of our robot's arm geometry. We found that because the rotational axis moved greater than 270 deg. normal potentiometers would not cover the entire range of travel. So, we replaced the standard potentiometers with continuous rotation pots.
Here is the "secret sauce" we used for scaling.
The robot controller supplies +5vdc to an analog input device. The Cypress board only provides +3.6vdc.
So we simple multiplied the sampled voltage from the Cypress by (5/3.6)=
1.389.
Here is the logic:
At one end of travel, both pots will give you 0vdc. At the other end, one will give you 5vdc and the other 3.6vdc. Both travel the exact same distance, so scaling is linear, just multiply the lower value by the scaling factor and now they are identical throughout the range of travel.