In PrestaShop version 1.6 in multistore mode, you have the possibility to associate your tax rules to specific stores.
The configuration will be passed onto Store Commander's interface, allowing you to display and select only the tax rule you would have previoulsy associated to the store(s).
The setup can be found in PrestaShop backoffice > Localization > Tax Rules.
When adding or modifying a tax rule, you can associate it to the stores by ticking the corresponding boxes:
In Store Commander's interface, the VAT drop-down menu will only display the rules associated to the shop you are working on.