Once you've created your taxes in BPro, you can apply them to orders on the 'Checkout' tab.  Above and to the left of the 'Accept Payment' button is a drop-down menu titled "Tax Rate Group".  If you click here, you'll see a list of tax groups you have created appear.  Clicking on one of them will apply that tax to the order.

Important Note: The 'Default' tax rate (if set) will apply on the first order for each customer.

Once you pick a tax rate for an order, future orders for that customer will automatically have that tax group applied!

After you have accepted a payment, the tax rate will be locked on this order and can not be changed.