You can for sure use either of the two methods you have mentioned but choosing between them would depend on your specific requirements and the user experience you want to offer.
Using deferred purchase options is a more integrated solution within the Shopify platform. It allows you to set a deposit amount at the time of purchase and then automatically charge the remaining balance at a later date. This provides an uninterupted experience for the customer as they don't have to manually make the second payment. However, this option requires the use of specific payment gateways, such as Shopify Payments or PayPal Express.
Creating a draft order for the deposit and then a second order for the remaining balance provides more flexibility in terms of payment methods and can be used with any payment gateway. However, this method requires the customer to manually make the second payment, which could potentially lead to missed payments or issues with order/payment management.