Get specific types of posts displayed in different sections of the page

I am using WP as a publishing platform, and need to modify it to be less bloggish and more CMSish. I am building the theme from scratch, and have created a layout with four columns (two of them for the main content). As in the News Print theme, the post on top of the page spans over the columns below it.

I want to be able to control what kind of content goes in which column: The space on top is reserved for the more important “sticky” stories and so on. I know my way around databases and understand the logic, however I’m not much of a poet when it comes to programming and thus I’m not capable of finding my way around the php bit myself.

Say I want to use the the space on top (that spans two columns) to display only the newest post, the first column to display all most recent posts in a reversed chronological order, and the other column to display posts of a specific category. (And of course I want to remove any redundant posts, so a single post is only shown in one of the three sections.)

Is there a not-too-hard way of doing this by php? Most of the functionality I want exists in the News Print theme, but I want to use my own.