Darker Than Black: Really confused?

I'm currently on season 1..just finished watching episode 13 and I pretty much get what's going on in each individual episode but as a whole it's really confusing. I have no idea how the different episodes fit together..will this eventually be revealed? I'm also a little bit confused on the relation between dolls/contracters and Hell's Gate. Also confused about what happened in South America. I just want to make sure I'm not missing anything important.