Categories are meant for general grouping of your events just like posts. It is used to sort and group content into different sections. Think of them as general topics or the table of contents for your site.
Label is like a badge and is set to your event when you want to inform your participants of any news on the event (e.g. event is canceled). Also, you can add a description to your label edit page and it will be displayed in the MEC single sidebar.