Marty,
1. The first thing you need to do is find sets of trucks compatible with your other trains. These will be 3 rail trucks with the 3 rail (large) couplers. MTH and Atlas both offer these.
2. Next comes the issue of what style of truck to buy. Go to your web browser and enter the name of the car you are researching and use the "images" tab to get pictures. Look at the pictures and match those with the ATlas and MTH offerings.
3. Another issue you will have is mounting the trucks to the car bodies. This is because 2-rail truck bolsters are made to scale so they easily fit the body bolsters on the body. 3-rail trucks have the body bolsters built into the truck bolster so a bolster on the body is not needed.
4. Also, 2-rail trucks usually mount from the bottom side of the car, as do the Atlas O scale trucks, while the MTH mount from the top. I recommend that you buy the trucks you want to use and then start the kits using the floor--make truck mounting the first thing you do on the kits before you do anything else. Create "rolling chassis" which are just the trucks and the floor and as few or none of the other details unless absolutely necessary at this phase of the build.
5. Another issue is that the large flanges on the wheels require the body to be mounted higher off the trucks than with 2-rail trucks. the flanges also can interfere with details or parts of the body, especially when on curves. You have to take this into consideration before starting the build. These compromise the prototype appearance of the car but can't be helped.
6. And if that isn't enough, end details may need to be left of order for the coupler to swing side-to-side when going around curves.