How are taxes handled in Deposits/Partial Payments?

Shopify adds the taxes on the checkout amount, which will be the Deposit amount if any clients pays for partial payment and the taxes will charged on the amount being paid while placing the order.

For the draft order flow, if the customer has an address in thier profile then Depo will add the taxes automatically. If there is no address then you can create the customer in Shopify -> Customer -> Create customer and can add their address.