Try replacing the comma (,) with the phrase "is a word":
EX: . . . panentheism is a word which holds that God is in everything.
pan (all), en (in) and Theos (God)
"God is in all/everything" (God made it all and so God is in every part of it all)
pan (all) and Theos (God)
"God is all/everything"
As for the comma before "but", there's this rule that says there should be a comma before conjunctions (e.g., "but" and "so") only if they are not directly tied to the sentence's main idea. In other words, the comma is optional, but necessary if the meaning the sentence expresses warrants one; i.e., a sharp transition: "[it] holds that God is in everything, but (it) also (holds that God) transcends the Universe."