To add a new custom tax rate please go to 'Settings > Misc > Tax Rates Country Specific'
You will see this screen.
To add a new tax Rate please click on green button labelled ‘New Tax Rates By Country’.
The above window will appear.
For example, if you’ve set a product to have a tax rate of 20%, but when you ship this item into Germany you want the tax rate to be 19%, simply select Germany from the drop down and enter the required percentage in the tax box.
Click ‘Save’ and this country specific tax rate will be used.