Matt,
I have worked with quite a number of Atlas cars and a few MTH. Atlas trucks do not have the same kind of bolster as MTH. MTH mounts the trucks from the inside of the car or bolster. the truck bolster is threaded and the body bolster is smooth. the truck mounting screw comes down through the car bolster into the truck.
Atlas trucks are mounted in a more traditional way with the mounting screw going up from the bottom of the truck. The truck bolster is smooth and the body bolster is threaded.
Both types use a unique (and different from each other) shouldered screw. Atlas actually has at least two types for metal vs plastic bolsters.
On the MTH cars, the body bolster has a large mounting hole and on the Atlas cars, the truck bolster has a large hole.
I have converted some MTH cars by just replacing the wheel sets. the fishbelly hoppers for example sit at the right height with just the wheel replacement and have good looking trucks. On the other hand, many MTH cars will sit too high on the track it you do this. You need to lower the car.
the best solution is to replace the body bolsters on the MTH car and then you can set them up to use whatever trucks you want. If you want to use Atlas, you probably need a much thinner bolster than if you use the typical 2-rail brands such as Athearn, IM, Weaver, and various brass ones.
You can also possibly fill or rebuild the bolster. You may have to remove material to lower it. You definitely have to fill the mounting hole and re-tap it.
Generally since you doing work in a place that is not usually seen, the job is not too bad. If you make some mistakes or whatever, they can be hidden. The first one takes a long time to figure out, but then it will go smoothly.