For each class in the taxonomy you can choose which attribute sets are applicable, and these sets will be inherited by default by any child categories unless removed. For example you may have the following Attribute Sets:
Default: Name, PartNo, Price, Images
Footwear: Size, Gender, Colour, Upper Material, Outer Material, Sole Material
Sports: Activities, Suitable for Indoors, Suitable for Outdoors
Which may be applied to the taxonomy as below:
To assign attributes to a particular class, select the class from the list and select the 'Edit' button, as follows:
This will bring up the 'Edit Taxonomy Class' dialog. From here, all attributes within an attribute set can be added to a particular product type by selecting the corresponding checkbox.
An attribute or attribute set does not need to be applied to all product types (unless this is the default attribute set). Attributes and sets can be added to any product types as needed for that taxonomy level.