Installing new rear axle onto existing driveshaft?

I will be getting a complete rear axle from a local wreckers to replace my existing one, but was just thinking after reading in the service manual about marking the pinion flanges when removing the drive shaft so that it can be installed the same way etc...

Well, obviously with a replacement axle, there won't be any way to know what the best way to attach the driveshaft to the new axle. I guess I'm looking for pointers on how to know all is ok and not out of balance and possibly destroying the pinion seal on the replacement axle from things being slightly off balance or something..

I hope you truck is safely up on jackstands rated for your truck's weight.
I don't see a problem but if you do sense a vibration in the seat or floorboard, remove the driveshaft at the pinion, turn the driveshaft 180 deg. then re-attach the driveshaft to the pinion.
More importantly, be sure the new differential is full of gear lube.

I will be doing it at a shop where I have signed up to apprentice for an auto tech. Just a small shop that does work on the company's cabs...but have hoists and all various jacks I would need. The old mechanic I am under will prolly know all about making sure its all balanced...will update the thread as I go.