A category can be added to a Flow board's side rail by editing the content in the side rail.
A user can add a category tag directly, and many of the metadata templates add categories.
Adding a category to a Flow board means that the board (Talk:Foo) appears in the category list.
Category tags that are added to the topic summary of an individual Flow discussion will not affect the Flow board categories -- those are only displayed on Topic pages.
If there are no categories added to the page, the "Categories" box doesn't appear. (same as with wikitext pages now.)
The design should look like the category box that currently exists on article pages, as seen below: