Hi,
I recommend don't modify any mojoPortal code or you will not be able to upgrade without losing your changes.
Currently the internal tax system only works when you are processing orders on the site using Authorize.NET or another card processor where payments are processed without the user leaving your site.
You must define a TaxRate (for specific states or regions), a TaxClass (ie Taxable, Non-Taxable), then you assign the tax class to an offer in the store.
If processing orders internally on the site tax will be applied after the user enters address info.
We don't currently support passing our own tax calculation to external payment sites like PayPal because we don't know the user's address and we do not ask for this information before sending the user to PayPal, so we have no basis to calculate tax since it is based on location. Typically PayPal returns that address data to us. So when using external payment gateways like paypal, currently you have to configure it in your PayPal account about tax collection.
Hope it helps,
Joe