I need advice on how to structure the categories according to the layout i have

It’s not really a category issue unless you want different areas to only show different actual categories.

What I’ve normally done in this case is either use custom fields or set up a custom ‘presentation’ taxonomy so on a post I can check a box to say “this post is a ‘Main Highlight'” or “this post is not-so-important” and then use multiple queries on the page to fill each of those post-areas. In your case one query for main highlight with one post, one query for secondary highlight with multiple posts, another query for secondary highlights (2) with multiple posts and then one final query for Not-So-Important with four posts. Doing it with custom fields is basically the same thing I suppose…

I try to keep the default categories clean because then I can output them on a post for thematic archives, without having presentational categories wind up in the list.

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