Since the Sesami App doesn't handle payments and all the payment flow goes through Shopify, you can use variants to define the payment method and mark the deposit or full amount as part of the booking information when the customer purchases it.
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Same as we have exemplified in this Demo Store: ROSE GARDEN BEAUTY SALON
The "remainder/balance" is a separate transaction you will do over Shopify, whether that takes payment in person or sends an invoice.