how to organize my categories or should I do custom post types for some?

I’d recommend going with a custom taxonomy, called “Semesters” (or “Quarter”, or “Issue”, or whatever makes sense in your context). You can then add “Fall 2012” and “Spring 2012” as Semesters, and assign posts to the relevant one.

(If you’re not interested in editing code to set up the custom taxonomy, the Custom Post Type UI plugin is a good one for that.)

From there, you can use any number of approaches to display content: you could create a custom archive page for the taxonomy, or check the taxonomy before displaying posts on the Main parent (and edit the query as needed), or create Pages with custom templates… the sky’s the limit, once you have them properly classified.