tkl8,
You are in an automotive forum, so can I assume yours is an automotive application, yes, good.
The reason so well stated by sreid is why you will see the engine, tran, and dif, as well as any in between gadgets, (such as retarders or aux gear boxes in large vehicles) all set on the same angle.
To minimize drive line angles, and hence u joint stress, the engine is set on an angle so as to "look" down towards the diff, which is on a lower elevation. If the engine were to be set level, with the tran attached, the angle to the dif would be horrendous, in u joint parlance, with miminal tolerance for suspension motion.
Therefore, if whatever you are doing that prompted your question involves automotive drivetrains, measure and maintain the design inclination of the drive train components to prevent u joint stress, and/or harmonics. If you get some component rotating with the angular acceleration/deceleration that the intermediate shaft between two u joints has, you will get harmonics, and/or vibration. That is what is created, and then cancelled out as so aptly noted by sreid.
With all the angles set correctly, your u joint still has a maximum angularity that it can operate at for the speed which you are trying to run it. You have to find that out from the vendor.
rmw