Look at the under side of the car/coupler. The rear of the coupler box has a slotted tab that holds the bottom of the box in place. I use 2 small sharp screw drivers to slip between this tab and bend it backwards away from the coupler until the bottom of the box snaps out. Then I remove the coupler and centering spring. There are 2 small screws holding the box to the body. Remove the 2 small screws and install what you want.
Alternately if you don't care whether the Atlas coupler survives, simply cut the tab away with a hobby knife or break it off with needle nose pliers.
Now the negative here is that the holes for the Atlas box are just a little short for the Kadee box. I use a drill (#43 I think) to elongate the hole in the REAR of the Kadee box until the holes will match with the Atlas underbody.
Atlas uses Metric screws - most times fine thread, but sometimes coarse. A 2x8mm screw will fit to install the Kadee Box. The 2 fits Atlas holes, and the 8 MM is long enough to mount the Kadee box.
Most times with 2 rail trucks, the couplers measure at the right height according to the gauge. However, on a few cars I have had to lower the couplers with shims.
