Yeah! I understand you mean! You understand some of the connection, but overall it somewhat still confusing. The Getbacker's plotline tend to be like that. Deep and Intricate. Like Caculus C, you understand what the equations are for but you aren't too sure how to use it...I did alright in that class, but still got a C...
Deep and intricate plot lines are confusing, indeed -- but that makes it all the more worthwhile rereading several times, because one always finds something new to understand!
And I really think that it's not going to be possible to fully "get it" until the very end -- I don't think even the Getbackers understand everything yet, either!