John Hayes:
It sounds like folks believe that the proper alignment for the prism is to align the edge of the prism to the edge of the sensor, but that's not correct. You want the prism to lie outside of the ray height for the sum of the chief and marginal rays at that location in the image train. In simpler terms, that means that the prism should not intercept any of the off-axis ray bundle at the prism position. If you don't achieve that, you'll wind up with a shadow of the prism at the edge of the field. Yes, flats should remove the shadow, BUT that's not good practice. Go ahead and follow the advice here but then back it out until your flats show no shadowing. The amount you have to back it out will depend on the focal ratio of your scope and on the size of your sensor.
John
So if my prism is as low as it can go, but is still not blocking the sensor even when it is on an angle, then I should be ok? No need to worry about making the long edge of the sensor parallel with the bottom edge of the prism?