We think alike, Sandi,that was my thought , to separate the maternal and paternal lines due to cousins, marriages, etc.
that is the way I have my paper files organized; I know some use notebooks but mine aren't that large yet.I also have file for Civil War, internet, correspondence, newletters,,,,,,same as you I guess.
From the replies I've received so far on this forum, it is thought best to keep them all in ONE big PAF file. Unanimous so far in that regard.
I also am a newbie (2 years), and due to family problems haven't been able to do much of anything for 6 months. My number one priority now is Organizing my paper files better, and entering data into PAF.