User categories are equivalent to sony collections. They permit you to build almost arbitrary groups of books listed in arbitrary orders.
They aren't the same as custom columns. A custom column holds data. A user category takes that data, creates named categories (there are tweaks to control the naming) and adds the books to the categories by looking at the data. In other words, it builds "groups" for data in the same way that calibre companion does for the standard fields (authors, series, tags, etc).
You group custom columns by entering the lookup key into CC using the "custom categories" dialog. In your case you would enter #read. HOWEVER, in the current version of CC only text-type custom columns can be grouped, so your yes/no column won't do anything. I have added support in the next release of CC for creating groups for yes/no columns in addition to the various text types.