Hello Ian,
Can Hikashop actually filter at the category level or does it just filter products?
Hikashop filter can only be used with products.The best solution will probably be to work on your product categories structure and on the displaying of the category listing module.
Also I can find nothing in the documentation that explains what the "attributes" field is in the filter setup - what does that do?
The "Attributes" option will enable you to add HTML attributes to your filters HTML code.
Thank you for your feedback, we'll update the documentation as soon as possible.