Additional Shipping Tax Options

In PrismCore Enter Mail Orders module use the hammer option, Select Manual Shipping Tax Override. This option allows you to select a tax amount to be applied to the shipping tax only, and that will override any other tax amount applied to shipping.
For example, if you taxed shipping at 10 percent as a default, and for this order need to tax it at 5 percent, you would pick the 5 percent tax type, and the system will apply 5 percent to just the shipping tax. The rest of the items will remain taxed as they were.
Before using this option, a tax code group should be created for each variation, with jurisdictions as needed, as well as item tax types. The item tax types do not need to be applied to any items, they just need to exist and have locations / POS's assigned to them so that they can be selected where appropriate.
Once this is done, you can use the hammer option Select Manual Shipping Tax Override. The list that is offered will be limited to only the codes that are within the Mail Order parameters applicable, including jurisdictions, states, etc. depending on how they have been set up.
When the tax code is selected, the shipping tax is automatically applied and the totals are updated. If you go back to the hammer option and select it again, the last tax code selected will be the one that shows when you first open the dialog (so you can tell which one was used).
Please note, in the case where the system was charging tax at a different rate than the items: The system looks at the item tax types for the tax to charge for shipping. If there is a tax code with tax shipping checked on ANY item tax type used on the order, the system will charge that rate for shipping. If there are multiple tax codes with tax shipping checked, the system is picking one and going with that rate. For now, the solution to this is to only have one tax code for taxing shipping, or to just make a tax code called shipping, add it to a tax code group called shipping, and add it to an item tax type called shipping. It does not have to be assigned to any items; it just needs to be there in item tax types. If there are different tax rates for different states/province/jurisdictions, then a shipping item tax type and code will need to be created for each one. You can only have one tax code with tax shipping checked for each state/province/jurisdiction or you will have issues with the amount of tax charged on shipping.
Also note, in the case where you have more than one mail order tax code group on the item tax type, if one is checked for shipping and one isn't, the system will use the one that is checked for shipping. Again, the system will just pick one if there are more than one mail order tax code group with tax shipping checked on ANY of the item tax types.
Finally, there is a parameter for pro-rating the tax amounts when there are non-taxed items on the order. The parameter is found in PrismCore Admin in the System Parameters module under the ship/receive filter. If checked, then the amount of tax charged for shipping is prorated when there are non taxable item(s) on the order. For example, if the tax amount is 7% and there are 2 items on the order, one is taxed, one is non-taxed, the tax amount that is actually charged on shipping would be proportional to the dollar amount of the taxable item.