It depends on creating the template correctly, that’s why most of the time using the invoices it’s better as you can make mistakes creating the account move template:
If you just put the accounts and the debit/credit amounts (like old fashion accounting), the taxes will not handled correctly (accounting will be ok, but reporting taxes will not).
If in the taxable lines of the account move you go to the form view you will see the Taxes tab to configure the specific tax, so then the tax reporting will be correct.
Sorry for the screenshots in Catalan, Impostos == Taxes.