Is there some kind of documentation about exactly what threshold values to use on various body parts to get the best segments?
if there is, how accurate is it, can it easily and cleanly separate things like skin, liver, heart and various organ tissues?
No sorry, it’s not exactly paint-by-numbers
If you are working with CT, this scale might help. If you are working with MR then mostly the images are not in physical units and only relative intensity values are meaningful.
I was afraid it would be an inexact science.
in that case, how would you do something like creating an accurate segment from a CT scan of a heart that has a hole in the side?
You could start with the tutorials - the second one on this list shows how to do a nice heart segmentation pretty quickly: