Create the sales order and add the items/shipping charges.

Add Store Credit as the payment and select "Charge payment upon shipment". There will be an error if you select "charge payment now".

Create the invoice.

Add the shipped lines to the sales order.

The Store Credit payment should be in the pending status.

When you complete the invoice, the store credit payment status should switch to complete and the amount removed from the customers store credit balance.
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​Note: store credit will still show up in the individuals account until the order has been shipped. While still in the account that store credit can be used for another purchase, but when the sales order is processed if there is not enough store credit there will be an error preventing the sales order being completed until a new, valid payment is added.