From the Settings (Admin Control Panel -> Taxes -> Settings) menu:
Apply Tax on Site Fees
If checked, enables tax for site fees.
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.
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 Account History (Home -> Members Area ->My Account -> Account History) and select the corresponding invoice:
Example: See below how to find taxes (the tax corresponds to the VAT tax described in the Configuration menu)