Originally Posted by
tsurara
RahXephon is not based on manga... it's based on a series of novels.
The manga is an adaptation of the anime, not visa versa. It's unlikely to clarify anything. All it does is provide alternate character designs, some stupid jokes and a lot more panties. At 3 volumes, it's an abbreviation of the anime series ~ not an expansion.
If you want clarification, you'll need to go to the novels.
Though I didn't find RahXephon to be confusing at all... What didn't you understand?