By default both your products and your Brands products will count towards your free shipping threshold. This was designed with the best customer experience in mind. Brand shipping rates will still be added separately for Brand products in the order. If you do not want Catalog products to count toward your site's free shipping threshold, you can navigate to Settings > Selling Preferences > select Integrated for your Free Shipping Contribution setting.
The separated shipping option does not currently work with 3rd party originated shipping rates (Ex: Recharge, ASR, etc)
*Note: For this feature to work you will need to download and onboard onto the Catalog for Brands app. You are required to have both apps for us to correctly calculate your cart's shipping totals. This is currently a Beta feature on Catalog.