Two questions:

If I am riding a triathlon bike solely for the use of time trialing how do I adjust the sitting? Do I set it up exactly in the same position as my road bike? If so, what is the purse of hanging on the nose of the saddle? It appears like the pros in the tour of france have mixture of nose hugging and scooting all the way back for their position...

Second, if I have a powertap on my rear wheel, but then cover it up with a wheel cover from wheelbuilder, will I still get an accurate rating? I've heard the carbon exposed pieces are actually used as sensors, not sure if this is true.

I recommend getting a proper professional fitting on your Time Trial bike to get the most out of your position and bike.

Just one example of the differences you will face:
Saddle height tends to be different from a road bike fit, at least if you measure to the same point on the saddle. Pro riders who have to TT under UCI rules have to keep their saddle 5cm behind the Bottom Bracket, which means they sit on the tip of the saddle to get in a proper position. Sitting on the nose of the saddle can lead to uncomfortable pressure on the perineum and the scooting around motion that you see in videos. Being farther forward means that your seat height will have to come up a little bit in comparison to your road bike.

As for the disc cover, it will not affect the readings of the hub at all. Your measurements will remain accurate as long as your zero your torque as usual.

+1
what he said!

Saddle height to the same point will differ due to changes in seatpost angle 75+ on TT bike compared to 71-72 on a road bike.

But you will often find there is minimal changes in saddle height (a few mm in my case) if you measure to the bit of the saddle you actually sit on (which will be different in TTing)

Sitting further forward or using a steeper seatpost promotes greater use of quads and less use of hamstrings.
Although you will need to train your legs to adapt to the new position as well, hence much of magnus backstedts berating of pro's for not riding their TT bikes enough in training (on eurosport UK coverage!)

A well respected and experienced fitter will be able to help you, best to see one that has experience of TT setups as well as some are just used to roadie setups. Retul looks very good and am tempted to get a fit with it, but the fit is only as good as the fitter, not the tools they use!