Once you start creating your own templates, sooner or later you'll need to create new categories in the Template Chooser or delete templates you no longer need. Pages doesn't offer "New Folder" or "Delete Template" commands in the Template Chooser; you have to manually make new folders and trash templates.
Pages keeps all the templates you've created separate from its assortment of stock templates. If you save your templates in the standard location, you find them in the My Templates folder by following the path : [home folder] Library Application Support iWork Pages Templates My Templates. Drag any templates you no longer need from the My Templates folder to the trash.
To add a new category to the Template Chooser, create a new folder next to My Templates in the Templates folder. Name it for your new category, drag templates from the My Templates folder into it, or choose it when saving new templates.