As stated before, a CV joint is a 'double' u-joint of sorts. The advantage of this is that it is self-canceling. That is, if the angle between the transmission output shaft and driveshaft is 4°, then each u-joint takes half of that, 2°, and thus, cancels out the increase and decrease in speed of the driveshaft. This means that the driveshaft will rotate at the same constant speed (hence, Constant Velocity joint) that the transmission rotates at, regardless of angle. Since the driveshaft is now rotating at a constant speed that means that we can just connect the rear end to it via a single u-joint with an operating angle of zero, right? Nope. Remember what I said earlier? When there is an operating angle of zero, the u-joint isn't properly being lubricated. In a case like this, it is best to use an operating angle of 1-2°. See the illustration below:

Image from http://www.4x4wire.com

The joint at the transmission is a CV joint. The joint at the pinion is a regular u-joint. It seems simple, doesn't it?

Multiple Shaft Configurations
Not so fast there Charlie. What happens when you have two driveshafts between the transmission and pinion? Well, it gets a little more complicated, but the object is the same. You want to cancel out the angles by the time you get to the pinion.

Another note: There is a difference between canceling out angles, and a zero operating angle. If your transmission points down at 3°, and the driveshaft points down at 1°, and the pinion points up at 3°, then you have cancelled out the angles, and the operating angles are not zero. However if the transmission points down 3°, and the driveshaft points down at 3°, and the pinion points up at 3°, then the operating angles are all zero, even though you have effectively cancelled the angles. The latter example is something you should not do.

Ok, back to the discussion. Now that we have down the basics of u-joint phasing, lets look at systems with multiple shafts. I'm going to just go straight to an example, and see if you can understand what I'm talking about.

Here is the scenario: The transmission points down towards the rear of the vehicle at 5°. The first shaft also points downwards, but at 3°. The operating angle between the transmission and first shaft is 2° (5-3). The second shaft points up towards the rear end at 2°. The operating angle between the first shaft and second shaft is 5° (2+3). Now, we take the first operating angle, and subtract the second one from it. Here, it would be 2-5. This gives us a -3. As I said before, there are no 'negatives', so we ditch the - sign, and we are left with a 3° operating angle that we need to have between the second shaft, and pinion. Since our second shaft points up towards the rear of the vehicle at 2°, this means that our pinion can either point up towards the front of the truck at 1°, OR, it can point down towards the front end at 5°. When the rear end points up, we add to the second shaft angle. When it points down, we subtract. 2+1 = 3, and 5-2 = 3. So either way, we have a 3° operating angle, which will put our system into harmony. See the diagram below: