The VAT code is assigned to the country code, which is in turn attached to customer addresses. In order to designate a different VAT code dependent on the company you choose you will need to complete the following phases:
Phase 1 - Create a new country
Let us assume for the entirety of this example that the customer is based in Germany. If you use company '0' then they will need to have VAT Code 3, and if you use company '1' then they will need to use VAT Code 4.
Click on Options
Click on System Maintenance
Go to System Settings
Choose GENERAL System Settings
Click on Country Codes
Press Ctrl+M to enter modify mode and press F4
Enter a new 'Code' and using Tab type the 'Country', 'Type', 'Currency' and 'VAT Code'. Ensure the new country code mirrors the Company you will use it for. (e.g. DE1)
You are not able to edit the code of the standard Country Code (DE), so if you wish to create a new Germany with the code DE0 to make the system clearer you can do so by repeating steps 6+7
Phase 2 - Creating a second customer address
Go to Sales
Click on Customer Maintenance
Search for your German customer within the quickbar
Click on the Edit Addresses button
Press Enter, followed by F4 to create a new address.
It is advised to add the '1' prefix onto you new address code. Once you have created this make all the details match up except from the VAT Code. You will set this to 'DE1' instead of 'DE'
Phase 3 - Creating the Sales Order
Go to Sales
Click on Sales Order Menu
Choose Sales Order Maintenance
Press F4 to create a new Sales Order
When entering the options, you can choose between different addresses for the customer. Use 'Address' for one company and 'Address1' for the other.