Hi,
I’m not completely sure I understood you correctly, but I think what you need is to set fee “Type” to “Percent” and “Value” to “3”. And at the bottom of the fee settings page, you can find “Taxes” options. There you need to enable the checkbox and set “Tax Class” to 6% tax class. Tax class needs to be created before that (you can do it in WooCommerce > Settings > Tax).
Again, I’m not sure, but maybe alternatively you can just set fee value to 3.18% instead if 3% (and do NOT check the “Taxes” checkbox). That is: 3 + (3 x 0.06) = 3.18% But I think the first solution is more “correct”.
Please let me know if that helped.
Best regards,
Tom