Gnucash can let you create taxation tables which represent on or more taxes and in which expense or income accounts
that the taxes must go.
It is important to create a different taxation table and tax account for customers and vendors, because the taxes you charge to your customers are incomes while taxes you pay to your vendors are expenses. They should therefore not get in the same account.
Thereafter, you will be able to apply a taxation table that you have created to any invoice you create or have already created.