To show included taxes in the invoice use the template variables [INVOICETABLEVAT] or [INVOICETABLEVAT2]
=== VAT - on extras ===
By default the system will apply the VAT rate set in SETTINGS->PROPERTIES->BOOKING RULES to all upsell items. If an upsell item has a different VAT rate you can set it in the "VAT" field in SETTINGS->PROPERTIES->UPSELL ITEMS.