What is the difference between the two characters of 自己?
自 self (adv)


Examples: 


自動(self move/ automatic)
自尊(self respect)
自助(self help)


動(to move), 尊(to respect) 助(to help) are all verbs, therefore 自 has to be an adverb


  己 [1] [pron] oneself; one's own; personal 



視天下事為己任 (see the world's affair as one's own responsibility)
視為己出 (treat as one's own child)
己所不欲勿施於人 (do not impose on others what oneself do not wish to be imposed upon)


己 is a pronoun in all three examples above. 


  自己 oneself; self (i.e. 我自己 = myself)


~


  but I do know that to know self is 知己, is one more the person and the other a different feature like a soul?


知己 (to know oneself)

知己者 (the one who know me/ confidant) often shortened to 知己

A famous quote from 《戰國策‧趙策一》: 士為知己者死  (A dignified man would die for the one who truly know him)

'know' here means 'truly understand'