From the Settings (Admin Interface -> Taxes -> Settings) menu:

Enable tax on Site Fees

If checked, enables tax for site fees.

Tax Type

Select the tax that will be applied to site fees:

Allow Sellers to Apply Tax

If checked, allows sellers to apply tax on their listings.

Front End

The selected tax will be automatically applied to site fees based on user location.

To see if the tax is applied to site fees go to Tools -> Accounting and select an invoice:

Example: See below how to find taxes (the tax corresponds to the VAT tax described in the Configuration menu)