Thank you all for some great questions and responses as they have helped me get this far. I'm hoping for a little more clarification though as far as taxes go when QBO is retrieving data from another web based software program.

The company I work for uses one program for all our business operations however we recently added QBO to switch over our accounting processes, leaving inventory in the original program. Both are web-based. I've set up our Sales Tax area and our Sales Invoices appear to be calculating correctly. Yet when we create an invoice in our old system, my understanding is that we leave tax off of the invoice and when it is retreived by Quickbooks, Quickbooks determines the tax to be paid (so automated sales tax is being calculated for each sales and purchases).  Each supplier expense is showing up 'out of scope' with no taxes applied. 

Can I please clarify, is tax to be applied to expenses BEFORE QBO retrieves the bill?