After struggling with this for almost a whole day I believe I can help explain the way Guides and Categories work, and how they can be organised.

Instead of thinking of a "folder/subfolder" analogy, you must realise that a guide is defined as being in a category by a setting in that guide. To move a guide to another category, you can't drag it anywhere. You must edit the guide, and change the category in the drop down box.

The same goes for categories inside categories. Even though there is a (very) basic content organiser in the Management section for administrators, you first need to have at least one category in the "Home" section, before you can rearrange subcategories.

This results in you needing a "bottom-up" approach: Make sure all your low level guides have their Category field correct, and that you have at least one Category in the Home level. Then you can drag categories around in the Management-Content section.

You must also be aware that you must always save, and refresh, since I've found many category changes were not realised or a guide was in multiple categories at once, until I refreshed and navigated around the pages a few times.