@3csrl
Hmm.. I am not sure why this is happening to you. You do not need to sue the shipping zones (woocommerce) at all. The Vendor Shipping can be used as a standalone method for shipping.
If you want to pass along an admin login & password in a private reply, I can take a look at the shipping.
Side note: You also need to update your theme. HandyStore overrides some of our templates, and those are now out of date. This will cause issues on your site.