On "modern" Atlas O trucks. First unscrew the truck from the car frame. Turn the truck over -- top side up -- and you will see one screw on each side holding the side frame to the rest of the truck. Loosen or remove one or both screws and then swap out the wheel sets.
If you're also installing Kadee couplers you may need to cut off/trim down the pumpkin knuckle coupler extension.
Another approach is to buy complete Atlas O 2 rail trucks and swap them and then sell the 3 rail trucks. The complete trucks and the wheelsets only are close to the same price and the 2 rail trucks are cleaner looking.
Also, you might consider the NEW Atlas O 2 rail trucks which are narrower and closer to scale. But, not many of them are available yet. I was able to get a dozen or sets from the initial production