The Tool Racks must be of the same type, or at least at the same height. The sole input for pick and place is the reason why they cannot be mix and matched. 

To properly get your tool height, you must get the machine coordinates of where the Z axis is when a tool holder is installed over a tool rack. If your position is too high, you'll drop the holder into the rack with a clunk, and fail to pick the holder up up. Too low and you could cause your bed some deflection, and ugly sounds coming every time you try to drop off and pick up. It is better to have it drop off an a hundredth of an inch too high, than it is to drive it down a hundredth of an inch too low.

When collecting your coordinates, it's important to use your machine coordinates found on the F2 and F3 screen as seen here: 

After you have your pick and place coordinates, you can collect your XY coordinates of all your tool rack locations and write them down or utilize the screenshot function of Masso, then proceed to Programming of ATC in Masso