Ok so suppose I have a monsters soul in a magic jar spell and I want to cast charm monster on it. Should I cast it on the soul in the jar or the monsters body? Also, does the monster retian his will save or should he use the one of the spell caster?
The soul is not technically a creature, so cannot be targeted by charm monster while not in its body (unless using some effect like astral projection). A charm monster cast on the monster's body will affect the mind inhabiting the body at that time (or the original creature's mind, if both minds are present, unless the other mind is deliberately targeted). If the monster is targeted (either in their own body or in another creature's body), they receive their normal Will save (as their mental ability scores do not change).
Possession effects are explained in greater detail in Occult Adventures.
Ok thanks
When a creature is possessed, they are essentially immune to mind effects. The only spell I can think of that could still target a creature that was being Magic Jar'ed or possessed would be something like Dream or Sending which doesn't really target them directly.
When a creature is possessed, they are essentially immune to mind effects.
That's one of the clarifications that Occult Adventures details (and I summarized). If the possessed creature's mind is not in the body (magic jar) it cannot be targeted by casting spells meant to target a "creature" (as a disembodied mind is not a creature). If the possessed creature's mind is still in the body (classic possession), then mind-affecting spells targeting the creature will still affect the creature's mind (assuming that the caster doesn't know about the possession to target the possessing mind instead of the creature's mind); however, it will not usually affect the possessing mind (unless it is an area effect or other spell that does not need to specify targets), which may continue to control the possessed creature's body (if the possessing mind is expelled or leaves before the duration of the mind-affecting effect ends, the formerly possessed creature is still under the effect).
The Most Interesting Man in the World:
"I don't always use Necromancy, but when I do, I prefer Possession."