This is a very tough problem. When there are 2 roller bearings on a machine the alignment can be very critical.
The consequences of poor alignment are axial forces. The axial forces from misaligned bearings will cause the rotor to spiral in the direction of the angle of misalignemnt.
If you are using bearings with added thrust flanges, these forces will not be noticed, but there will be internal skidding in the bearing and at times of poor lubrication the bearing can fail. Try to use a combination of ball to carry the thrust load and roller for the radial loads. If you part is very heavy, Spherical rollers may be your only choice