Another question when holding bolts in a chuck how do you protect the thread from getting damaged
This depends on whether or not the unthreaded part has some form of drive.
If it's a bolt (or you're making it into a bolt), you'd be best off making a long holder for it. When you're done, you can unscrew it using the head for drive. This method may lock the bolt into the holder because of the cutting action tightening the bolt. It almost certainly will in a lathe.
If there's nothing to grip to unscrew it (like a particular part I make) you can use 2 nuts locked together.
This is so that you can grip the threaded part away from the end of the thread, meaning you can remove the nuts easily once they're unlocked.
A more accurate variant would be to make a holder shorter than the thread, and larger diameter than a nut, and lock a nut on the end.