Ghost has a single, powerful organisational taxonomy, called tags.

It doesn't matter whether you want to call them categories, tags, boxes, or anything else. You can think of Ghost tags a lot like Gmail labels. By tagging posts with one or more keyword, you can organise articles into buckets of related content.
Basic tagging

When you write a post, you can assign tags to help differentiate between categories of content. For example, you might tag some posts with News and other posts with Cycling, which would create two distinct categories of content listed on /tag/news/ and /tag/cycling/, respectively.

If you tag a post with both News and Cycling - then it appears in both sections.

Tag archives are like dedicated home-pages for each category of content that you have. They have their own pages, their own RSS feeds, and can support their own cover images and meta data.
The primary tag

Inside the Ghost editor, you can drag and drop tags into a specific order. The first tag in the list is always given the most importance, and some themes will only display the primary tag (the first tag in the list) by default. So you can add the most important tag which you want to show up in your theme, but also add a bunch of related tags which are less important.