For VAT management, you can declare the different VAT rates in WooCommerce as explained here: https://woofrance.fr/guide-utilisateur-woocommerce/2-options-et-parametrage-de-woocommerce/options-des-taxes-tva/
You can then go to the settings of WC Accounting: WooCommerce > Setting > Accounting > Taxes and delivery options to define the specific account number for each VAT rate.
The procedure is identical if you wish to establish different accounts corresponding to the different types of delivery that you propose.