Youre just adding extra thread length? Yes, hold it in a vice with the rod vertical, but with the threads as close to the vice jaws as possible - as in, dont clamp on the opposite end of the rod leaving a long, unclamped length (this COULD cause twisting). Use some sort of cutting oil or WD40 and take light cuts (twists) before backing out the die to clear the chips. Just take small passes at a time with plenty of oil and you should be fine
