I assume you're replacing the prop shaft u-joint (and not the axle u-joint). To drop the prop shaft out you will also have to drop the exhaust pipe. And as mentioned in an earlier post, make sure to mark the current prop shaft alignment relative to both differential and transmission mounting flanges, as well as the yokes on the prop shaft itself, to maintain current shaft balance.
I used a (big) hammer on the drive shaft yoke to pop the bearing cup out. Its preferable to use a vice or a u-joint remover, as noted in other posts, but depending on how long they've been in there, the bearing cups can be pretty difficult to get out. I wound up having to use the hammer, but I would try squeezing them out in a vice first.
When you install the new u-joint, make sure the grease zerk is facing the front of the car. Also, if you have a good look at the prop shaft yoke, you will notice one side seems to be more 'cut away' than the other. Hard to explain, but you'll see what I mean if you look. That extra cut-away area is to allow access to the grease zerk. So you have got to install the new u-j with the zerk facing forward AND make sure the zerk is on the correct side of the prop shaft yoke, so you can actually get at it later with a grease gun.
When you install the new u-j, make sure the retaining circlip engages fully in its yoke or flange ring. I have had a circlip pop out on me (not the prop shaft, but on an axle), and the bearing cap just follows it right out. No fun to drive and even less fun having to redo it it all.
Truthfully, if I had to do it all over again, I would just drop the drive shaft and take it to a shop. Getting the drive shaft in and out takes the most time, and removing and installing the u-joint takes the most expertise, so on balance I would just let the pro's do the u-joint part.
As far as the flange nuts are concerned, you shouldn't need a torque wrench. They only tighten down so far, and then that's it. Use new nyloc nuts, and tighten them right up.