To make use of the shipping quotes you need to fill in the complete address at the top of the globals file. Once you have done that you need to enable shipping with this setting:
$WAGLOBAL_Shipping_Enabled = true;
If you are using UPS you need to ensure that you have the shipping variable set like this:
$WAGLOBAL_Shipping = 1;
Other than this you just need to fill out the details for your UPS account correctly. You should see the shipping charge when you get to the confirm page but not before this.
For the state tax you just need to fill in the tax rate as a decimal value then the state to charge tax in. You would enter the standard two letter abbreviation for the state. If you leave the state blank in the globals file it should apply tax regardless of the user selection.
To disable the credit cart checkout you could just hide that part of the checkout page with some php code, you could then enable it by changing the code back. The form is on lines 429-1659, if you added some code like this before and after these lines you could get the form to not display:
<?php /* ?>
<?php */ ?>
You could then just remove this extra code to get the form to show again if you need it.