Categories and brands
Commerce Kickstart is a 'canned' solution, so you're limited by what's been 'hard-coded' already. This is fine, you just need to make some leaps of faith to use their product for your purposes. 

You can't use the hierarchical structure of 'indented' sub categories of a Drupal taxonomy as an expected subcategory in Commerce Kickstart. It just doesn't understand it (yet). Unfortunately, you can only use a single level of category for each taxonomy category term. In Kickstart 2 - that's called the 'Collection' taxonomy. So don't add subcategories there and expect them to be shown. In some ways, this saves you some headaches.

You need to make a separate (again, single level of depth) taxonomy term for subcategory. You also need to set it to be a taxonomy of product classification (the checkbox thing in the Edit of the taxonomy). 

With both separate, single level of depth, taxonomies, you then need to add these term reference selection boxes to your 'Product Variation' (and NOT Content Type). 

You then need to put your brand, set up the same way as the other two, mentioned above, in your 'Content Type' (NOT product variation).  

You then need to set up all of your Display Views, in both Content Type (CT) and Product Variations (PV). Look at the 'Tops' CT/PV set up to match that setup for guidance.

In this way, the 'All Products' view will work to allow you to filter by all terms of category, subcategory, and brand... or what ever other classification you can think up.